I have so far tried using Pandoc to convert Markdown text containing LaTeX math to ePub with MathML. This works, but the resulting math displays quite horribly compared to what the corresponding math looks like when generating PDF from LaTeX. For example, upper and lower limits of an integral do not align well. I have tried using Calibre too and here it is actually possible to convert the math to MathJax-viewable format, but it seems I cannot rely on other ebook readers to be able to use MathJax. Besides, this only worked when converting from HTML, not Markdown.
Update: @karsten-w's answer made me think more about embedding the maths as graphics. I found out that ePub seems to support SVG, at least ePub from v. 3.0 according to what I stumbled across. So for example, I can generate the math SVG from LaTeX using http://www.tlhiv.org/ltxpreview/ (see https://tex.stackexchange.com/questions/103282/convert-latex-to-svg-online). I can then easily embed the SVG in Markdown and convert to ePub using Pandoc.
Now I would just like a smoother workflow that can take me directly from LaTeX with maths or Markdown with LaTeX maths to ePub with embedded SVGs...