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Your CCD numbers seem way too optimistic to me. Also, I believe that the eye is somewhat more efficient. But it doesn't matter all that much, the fact that with a camera, you can integrate the light over a vastly longer period seems much more important to me.

A typical 8 Mpix sensor would be much better as a 2 Mpix sensor of the same total detector size and sensitivity ... So if you have a crappy electron well that can hold 10^4 photoelectrons ...

That's all fine, but what really matters how many more electrons the well will hold if you make the sensor pixel 4 times larger in area and how many more photoelectrons you can generate at the same exposure settings. If both of them are scaled by a factor 4, you can just as well average four adjacent small pixels to create a lower-resolution image.

Of course this averaging should be done in the camera/phone firmware before the JPEG compression step.

Not so; the averaged pixel would be noisier than a larger pixel of the same area as the aggregate even if the number of detected photoelectrons scaled perfectly.

I mentioned only photon shot noise, but other sources of noise exist in CCD and CMOS detectors, and their effects are additive (in a mean-square fashion). In particular, readout noise and bandwidth noise will make the situation worse if the same number of photoelectrons are divided among more pixels. Bandwidth noise increases with the bandwidth at which the chip operates; with four times as many pixels, the bandwidth must be higher to get an image in the same time, so the bandwidth noise will be higher per pixel. Similarly, readout noise depends on the number of pixels to be read, and is higher for four times as many pixels.

In aggregate, the noise in detectors which are equal in area and sensitivity will be rather higher if that area is divided among more pixels. Aggregating four pixels into one after readout does not help much. The aggregated pixel will always have a worse signal to noise ratio than a single pixel of the same size as the aggregated pixel. You could try reading this to get a basic grip on imaging noise. Or use your google-fu.

This might be a good component to check out .. :)

This is why I read down before I reply. You beat me to it. From the full image height spike and what appear to be after-images at regular intervals I would say you are dead on. The CCD went WAY beyond saturation for that moment. Not a lens flare, but still very impressive.

Fairly informative article on the subject here:
http://learn.hamamatsu.com/articles/ccdsatandblooming.html

I noticed in a book I am reading, Schrödinger's Kittens, it mentions the work of scientists at Hamamatsu who published their work on the wave-particle duality of photons.

So there are corporations involved in hard science.

the only option is to buy another Laue diffraction machine to replace the one we have

That's hardly your only option. You can modify the machine to use a digital sensor instead of film. There are off the shelf sensors:

http://sales.hamamatsu.com/en/products/solid-state-division/x-ray-flat-panel-sensor.php

so it's mostly a matter of choosing the right one and doing a bit of mechanical engineering to mount it in place of your film camera.

What is a "themos cow" and why does it have its own newspaper?

It's proof that the vacuum tube is alive and well... "9600 PMT detectors". Let's see a silicone detector do that.

For a good reference on PMT's goto http://www.hamamatsu.com. I'd be willing to bet they made the PMT's.