Would it be possible to have a jumper (or maybe do it via software, I don't know) to enforce 1:1 pixel scaling? For example, assume you have a period appropriate 19" LCD at 1280x1024. The video card would always send a 1280x1024 signal. But when you "change" the resolution on your Mac, instead of actually changing the output signal (it'll keep it at 1280x1024 at all times), it'll compare the 1280x1024 output to the requested "resolution change," then produce the maximum 1:1 scaled image it can output. Fill in the remaining pixels with a black border (or perhaps a user selectable color like on the IIgs.)
So assuming you have said 19" LCD at 1280x1024 and you switch the Mac to 640x480, it'll "change" the resolution to a pixel doubled 1280x960, then fill in the remaining 64 pixels on either side with black (or whatever color.)m Or let's say you're playing a really old game that wants the original 512x342. It'll "switch" the resolution to 512x342, but in actuality will pixel double both the vertical and horizontal to 1024x684, then fill in the remainder with the border, all while maintaining the original 1280x1024 output.
That way the image you get is always a perfect 1:1 scale with no interpolation.
Hope that makes sense.