I have made a new patch that might help with this, see
this post in the developers forum.
If JSWolf's idea works then that might be better because you can just remove the embedded fonts from the books that have problems and leave the good ones alone, but the patch's advantage is that it should work with books downloaded direct from OverDrive too.
There is no way to distinguish between library books and other sideloaded ePubs though, so the patch will affect all ePubs. It shouldn't affect KePubs though, as they use a completely different system for selecting fonts.