Andy,
Why not have the camera capture two exposures on the same sensor, one right after the other, without the mirror moving between exposures. Perhaps the user sets two sensitivity levels, one for each exposure, for example: 100 ISO and 800 ISO and then the camera selects the best pixels from either exposure and combines them into a final saved image using a technique similar to that used by GLuijk in the "Zero Noise technique" thread.
Of course, it would double the total time needed for a single exposure but in the right situation this may not be a problem at all.
Mitch