I've not experienced that issue with Typekit fonts and IDML. Typekit fonts are really nothing different except that they are licensed not to be able to be packaged. They are just regular OpenType fonts.
I'd start by restoring your InDesign preferences first just to see if that fixes the problem. Here's how:
For anyone else who searches and finds this... I am experiencing a very similar (maybe same?) issue, when trying to export PDFs. It seems as though any time I try to export a file with Typekit fonts in it, InDesign crashes. I can't say for sure it's the Typekit fonts that are doing it, but there does seem to be a very strong correlation. Restoring preferences didn't solve it.
I have had success outlining the suspected fonts and then exporting, but that isn't always a reasonable option.
The more useful thing I found is that if instead of "Export" I choose "Print" and then choose "Adobe PDF" in the Print dialogue, I can then "export" successfully, without crashing.
Hopefully this might help someone out. And to someone who knows more about how the software works, (Adobe rep?) it might even shed some light on what's actually causing it in the first place...