I’m not sure this is a real answer, but have you tried PHP-markdown-extra (by the very same Michel Fortin)?
At least for me (using Mark Jaquith’s markdown-on-save plugin) your example is not a problem.
But Markdown-extra is not perfect either and I’ve seen some other quirks with respect to emphasis, e.g. Let $(y_n)_{n\in \omega}$ enumerate ${ x_i: i \in \bigcup_{n\in \omega} A_n} $ will trip it up.
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