If you have a look at books about maths and physics which have their official Kindle versions on Amazon, eg.
this one (click the cover to see a preview), the regular text is OCR'd but the mathematical symbols and equations are left intact, as images.
Would it be possible to do something similar with k2pdfopt? Right now the two options I've found are to leave the original text in and deal with a huge PDF file, or to leave only the OCR'd text and lose all equations.