I can think of a couple of ways:
PlasTeX + manual .epub manipulations. See:
Is there a PlasTeX custom-renderer which can produce ePub (or nearly ePub)?
@salimfadhley Did you end up going this way?tex4ht / latex2html / etc. See: LaTeX document to epub or mobi ebook formats (with mathematical formulas)
MathJax rendering on
.epubdevices which run js. But what about the fonts?
I am not sure which way to go though and I would appreciate any pointers.