This has bugged me for a long time. Unfortunately, there doesn't seem to be any easy way to fix it on the client side, since the MathJax markup is already mangled when it's sent from the server.
However, there's a (relatively) easy way this could be fixed on the server:
Make the "rendered output" diff engine treat MathJax blocks as atomic units.
The server-side Markdown parser is already MathJax-aware (since it needs to disable normal Markdown parsing within MathJax blocks), so this would seem reasonably doable.
The obvious down side of this solution is that even small changes inside long equations would be shown as the whole equation changing. Alas, there seems to be no way to fix that without somehow embedding diff support within MathJax itself. Fortunately, those kinds of changes are usually best viewed in source diff mode, anyway, and at least this would still be an improvement over the current broken rendering.