From what I understand, displaying Math symbology appropriately in a flowable ePub is VERY difficult...that was one of the issues that ePub3 solved. It can easily display the MathML. The problem is finding reader support for ePub3.
There seems to be some method of using mathjax...but I haven't delved into that area too much yet. You might be able to find some info here:
http://www.mathjax.org/resources/epub-readers/
Cheers,