I'm not familiar with how the video is encoded, but maybe you have to be careful to make sure that the encoding doesn't introduce correlations between adjacent frames (you can imagine how P or B frames might have correlated noise, for example).

Also, I don't think you'll ever see Cosmic Ray interactions last more than one frame... the time scales for cosmic ray interactions are in nanoseconds, not ms. I suppose electrons could get trapped somewhere and diffuse slowly (that does happen in some CCD's, I don't know enough about CMOS sensors to know if that can happen), but that would happen with bright images in addition to cosmic rays.

In such a small sensor, cosmic rays should be relatively rare. To first order, you can model the number of cosmic rays you see as a Poisson process, which should be a pretty good source of entropy. You can even estimate the rate based on altitude / sensor orientation, etc. However, nearby cosmic ray detectors will detect correlated cosmic rays (from extensive air showers from the same primaries), which might hurt.