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It may be too late, but you could tell your friend about vitamin D, iodine, and vegetables, fruits, and beans, as well as fasting, in preventing and sometimes curing cancer. I've posted many links on that stuff here in the past. Just google on those term and cancer, and look up Dr. Joel Fuhrman's work and Dr. John Cannell's work. Unfortunately, the best way to deal with cancer is to prevent it by helping the human immune system deal with individual cancer cells before they proliferate. Once you have cancer, things are pretty iffy. Fasting can also help in reducing nausea from chemotherapy. Good luck to your friend. Assuming the surgery is a success, exploring these things may help prevent a recurrence. Some links to start:
http://www.vitamindcouncil.org/health-conditions/cancer/
http://www.drfuhrman.com/library/article24.aspx
http://iodine4health.com/disease/cancer/cancer.htm
http://www.webmd.com/cancer/news/20080331/fasting_may_improve_cancer_chemotherapy
http://www.marksdailyapple.com/fasting-cancer/

Unfortunately, instead of scientists studying what is proven to work (nutrition, fasting, and lifestyle) and then people lobbying to make good support for healthy choices readily available to all, scientists seem to be creating what could become the basis of a weaponized plague that evades the human immune system. :-(

Look into iodine, vitamin D, and eating lots of vegetables, fruits, and beans:
http://www.iodine4health.com/special/metals/metals.htm
http://www.vitamindcouncil.org/about-vitamin-d/how-to-get-your-vitamin-d/vitamin-d-supplementation/
http://www.huffingtonpost.com/dr-mark-hyman/autism-research-discovery_b_794967.html
http://www.drfuhrman.com/library/foodpyramid.aspx

I applaud your caution, but I lost about 50 pounds following that sort of advice, and feel a lot better, and have kept it off easily. His book is probably the most scientifically based one out there... YMMV.
"Eat to Live: The Revolutionary Formula for Fast and Sustained Weight Loss"
http://books.google.com/books?id=CX8huSU0n8AC

Getting a good blender and making green smoothies helped a lot too.
http://greensmoothierevolution.com/

Dr. Fuhrman's approach can cure most type 2 diabetes too, but I doubt you will believe that either: :-)
"Dr. Fuhrman Cures Diabetes - But Drug Companies Object "
http://www.youtube.com/watch?v=46_GInjBeQU

But that is more and more common knowledge, except among most doctors and CEOs of drug companies:
http://www.rawfor30days.com/index4.html

His approach can also reverse most heart disease... Although others can do that too, as well. Just Google on reverse heart disease.

Is Dr. Fuhrman's approach perfect? No, I think it could be improved in a couple of ways. For example, I think he is a bit low on Vitamin D and quite a bit low on iodine. Others on that:
http://www.grassrootshealth.net/recommendation
http://www.iodine4health.com/

Iodine especially is a potentially big issue because if you eliminate salt and dairy as he suggests, those are two major sources of iodine in the US diet, and you need to replace that with a multivitamin or eating seaweed or other things. If you were under his care, he would no doubt check for that, but for someone following his advice from a book (myself included) it is easy to mess up on iodine. I brought that to his attention through his forum but he was somewhat dismissive of it, sadly.

I also think Dr. Fuhrman could prioritize his approach a bit better, and also that there may be issues about metabolic types and individual biochemistry that may come into play. It's also not clear if salt is quite as bad as he says it is.

In general, I think he has done a great job, but no one knows everything about such a complex topic. And his active practice probably also limits his time for additional study. I also agree with you that financial conflicts (he sells branded food products, even though he gives some of the proceeds to nutritional research) muddy the water. But that is also a big issue in our society in general, and we need something like some mix of a gift economy or basic income or 3D printing and/or great central planning to move beyond it.

But overall, he's probably one of the best out there, after having read tons of stuff by different people in my own quest for health for myself and my family.

Dr. Andrew Weil has better holistic advice, but not quite so good nutrition advice. He is also more knowledgeable on herbal remedies:
http://www.drweil.com/

Dr. Mark Hyman probably has better overall advice about autism:
http://www.huffingtonpost.com/dr-mark-hyman/autism-research-discovery_b_794967.html

We are in the midst of a revolution in nutritional knowledge and the connection to health, but sadly most people are in denial about it. And there are, as you say, so many vested interests and conflicts of interest that it is hard to know who to trust.

But as I quote here from Marcia Angell, the problem may be even worse in mainstream science:

And get probably 75% of medical issues diagnosed and cured, as they are mostly nutritional deficiencies... :-)
    http://www.drfuhrman.com/library/foodpyramid.aspx
    http://drfuhrman.com/library/article16.aspx
    http://www.vitamindcouncil.org/treatment.shtml
    http://www.grassrootshealth.net/

Sure, Omega-3s and Iodine are important too:
    http://www.guardian.co.uk/politics/2006/oct/17/prisonsandprobation.ukcrime
    http://www.iodine4health.com/
    http://www.bluezones.com/

As is a good night's sleep, friends, family, a connection to that which is beyond us, meaningful work, daily exercise walking and such, and that kind of stuff. And obviously avoid smoking, excessive alcohol, and obvious environmental toxins at work and play.

The focus on magic bullets is unfortunate. As is a focus on diagnosing things like cancer, heart disease, and diabetes that are mainly signs of vegetable deficiency disease and lack of vitamin D (and to a lesser extent those other issues). Most health rests on the basics. It's true that there are exotic genetic diseases and so on, but what causes the most chronic misery and early death in the industrialized words is these basic nutritional (and sunlight) problems.

Still, for cheap testing, this may be the future through using a paper-with-chemicals test and a cell phone, and such tests could help detect nutritional deficiencies:
    http://www.ted.com/talks/george_whitesides_a_lab_the_size_of_a_postage_stamp.html

Of course, there is not much profit in actually preventing or curing disease, so most of the money pours into diagnosing and treating what are really symptoms of nutritional and lifestyle disorders... It's been that way in part since the misguided Flexner Report:
    http://en.wikipedia.org/wiki/Flexner_Report

But yes, this is still a great initiative -- even if it misses the obvious. But there is so little that is obvious (as is said in the Skills of Xanadu): :-)
    http://books.google.com/books?id=wpuJQrxHZXAC&pg=PA51

And of course, in our widely dysfunctional and dying culture, where people mostly eat either long dead carrion (aged factory farmed meat) or ground up long-dead plants (flour and sugar), and much of our entire cultural socio-economic infrastructure is geared around getting everyone to embrace this death-eater cult, it is no metaphorical surprise that the result of being a death eater is that you die early... Related:
    http://www.seriouseats.com/2007/11/the-subsidized-food-pyramid.html
    http://www.diseaseproof.com/archives/diet-myths-the-food-pyramid-of-the-insane.html

Do you really need a "tricorder" to diagnose death-eater disease?

http://www.vitamindcouncil.org/health/autism/autism-information.shtml
http://www.vitamindcouncil.org/cancerMain.shtml
http://articles.mercola.com/sites/articles/archive/2010/07/22/pregnant-women-advised-to-get-more-vitamin-d.aspx
http://www.iodine4health.com/

Both are involved with immune function in different ways. Adequate vitamin D is needed to make the brain's master antioxidant, glutathione. Adequate iodine helps excrete heavy metals. Both are involved with zapping cancer cells (it's said the average adult gets one cancer cell a day, but a good immune system deals with it). Vitamin D is essential to preventing pregnancy complications, including C-sections.

The US RDA for iodine may be way too low, especially considering how much bromine and fluorine kids are exposed to. The vitamin D RDA is also too low, even with being recently revised upward.

Eating fruits and vegetables also helps preventing lots of disease and is essential to good health.
    http://www.drfuhrman.com/library/foodpyramid.aspx
    http://www.diseaseproof.com/archives/diet-myths-the-food-pyramid-of-the-insane.html

One can tease out a lot of the individual nutritional and environmental causes in some cases of autism:
    "Autism Research: Breakthrough Discovery on the Causes of Autism"
    http://www.huffingtonpost.com/dr-mark-hyman/autism-research-discovery_b_794967.html

Let's get that all right before arguing too much over other stuff and what the true risk/reward assessment is for otherwise healthy kids and vaccines. A focus on magic bullets may be leading us to miss the big picture here about optimal health, which is earned by eating right and a lot of good lifestyle choices.

If pediatricians educated parents more about nutrition, we'd probably have a lot healthier population, even without vaccines.
"Disease-Proof Your Child: Feeding Kids Right"
http://www.amazon.com/Disease-Proof-Your-Child-Feeding-Right/dp/0312338058
"A groundbreaking book that explains the connection between nutrition and disease prevention-showing parents how to keep their children healthy by feeding them right. Bombarded by the media with stories about childhood obesity and dangerous hormones, pesticides and additives in foods, and told that allergies, asthma, and ear infections are on the rise, parents have never been more concerned about what to feed children. In this invaluable resource, featuring easy-to prepare, tasty recipes, Dr. Joel Fuhrman explains how cutting edge nutritional science can be brought to the family table with amazing results. "

See also for how to break out of the junk food pleasure trap:
    http://drfuhrman.com/library/article16.aspx

Please see my other posts to this article, including these links and others:
http://www.huffingtonpost.com/dr-mark-hyman/autism-research-discovery_b_794967.html
http://www.amazon.com/Disease-Proof-Your-Child-Feeding-Right/dp/0312338058
http://www.ravediet.com/preview.html
http://www.iodine4health.com/

The first link suggests that pretty much all autism is related to various issues like you discovered in time (there are just a bunch of them from vitamin D deficiency, to iodine defiency, to lack of omega-3s, to dairy, to toxins of various sorts in processed foods or, presumably, vaccines). From there: "Most neurodevelopmental disorders have common roots. But looking at only one aspect of such conditions will not solve the problem of autism. Current autism research is based on an outdated approach -- one that is something like blind men examining the proverbial elephant. Each researcher works in his or her own silo examining different factors and coming to different conclusions. Research that integrates, synthesizes and examines all the data on causes and potential treatments is practically non-existent. The mitochondrial dysfunction identified in the JAMA study I've been talking about is ultimately only one downstream symptom of many upstream causes. Other researchers have found systemic inflammation,(ix) brain inflammation,(x) gut inflammation,(xi) elevated levels of toxins and metals, gluten and casein antibodies,(xii) nutrient deficiencies including omega-3 fats,(xiii) vitamin D,(xiv) zinc, and magnesium, and collections of metabolic dysfunction related to quirky genes that make it difficult to perform chemical reactions essential for health in the body such as methylation and sulfation.(xv)"

The second and third links show why excessive dairy is pretty harmful for most people (even ignoring how most of the world is lactose intolerant). The fourth is something I'm just learning about at the moment (iodine deficiency, where dairy is often a primary source of iodine, so watch out for it without dairy or eating seaweed or supplementing).

Your son is lucky to have you as his Dad. You might want to still monitor for the other health issues and take pro-active steps to "disease-proof" your family on a diet of mostly vegetables, fruits, and beans (and some nuts, seeds, and whole grains).

As a four year old, my wife had surgeons open up her belly and take her guts out (and put them back) because they refused to listen to her mother who suggested she had a millk allergy (from an article she read) -- and it turned out, after all the trauma, yes it was an allergy to milk and lactose. Doctors (especially surgeons) seem to be trained to sound very confident even when they don't have a clue (especially about nutrition). Part of how it got that way, starting around 1910:
    http://en.wikipedia.org/wiki/Flexner_Report

For down the road:
    http://www.newciv.org/whole/schoolteacher.txt
    http://www.holtgws.com/

http://science.slashdot.org/comments.pl?sid=1932134&cid=34740048
http://science.slashdot.org/comments.pl?sid=1932134&cid=34740098

Also, from:
    http://www.corpwatch.org/article.php?id=14401
"Merck spokesperson Amy Rose refused say how many trials Merck contracted to CROs or what percentage of the Gardasil subjects these contractors recruited in the Third World. She also refused to specify how, or even if, the company oversees CROs. Many consumers assume that the FDA carefully monitors CROs. But the agency hobbled by under-funding, politicization, and dependence on industry fees has few resources to assess foreign trials and relies on drug companies. "

On the point in your sig, and maybe a way to get better research by less conflict-of-interest in funding:
    http://econfuture.wordpress.com/2010/10/19/robots-jobs-and-our-assumptions/#comment-392

On keeping people healthy for cheap:
    http://www.amazon.com/Disease-Proof-Your-Child-Feeding-Right/dp/0312338058
    http://lewrockwell.com/sardi/sardi111.html
    http://www.iodine4health.com/
    http://www.ravediet.com/preview.html
    http://www.bluezones.com/

But that's the problem -- there are no enormous profits in natural wellness; the only big profits are in palliation and treatment for sickness or random attempts at "magic bullet" wellness through phrama stuff.