This is a tricky one, and I can't really say how it will be solved in the future but we'll have to figure out something.
The inability to render questions is kind of a major deficiency (if one that didn't exist until well after 1.0 was frozen).
This has been added in 1.1.
/1.1/sites reports markdown_extensions with values Prettify, MathJax, and jTab as possible returns. However, new extension can be added at any time.