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It's more to do with the mathjax using features of html+css which are not supported by mobi/kindle. You could embed the html+css or MathML in epubs, however then you will run into compatibility issues with the various epub renders. The safest would be to use MathML and a fallback rendered image. The image would be used on kindles/mobi, while if in the future some of the common epub renders start to support MathML, they would then display that.
At the moment there's no easy way of doing this. For a project I did a while back, I used a script to generate all of the MathML -> png's via a public interface on WolframAlpha, however I just checked and it seems to have been removed (it wasn't really documented anyway).
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