This potential problem is overstated if the quality of the scans is decent. I have scanned literally hundreds of books, and encoded them in both djvu and pdf/jbig2 formats, and have never once found a bad character. (Yes, having heard of this issue, I did initially try to find examples) The free djvu tools have parameters you can adjust to make them more or less aggressive at combining similar characters, and above 200DPI it's hard to even force the issue to happen for something like an 8 versus a 6. That was my experience anyway.
It's also telling that the example trotted out is always a decades-old photocopier implementation. Unless someone does some comparisons of recent scans and finds a bunch of altered characters, I just don't buy this concern. MRC+JBig2 is really great and the size savings have not been trivial for me personally.
(I hesitate to add that the alternative would be, I assume, DCT/jpeg page images, which introduce lots of noisy artifacts of their own... destroying our history one DCT-block at a time!)