I think the only problem area you would run into is with subclassing the View class, because it does some funky things with jQuery. Those are problems you can work around though. Other than that you shouldn’t run into any other problems if you use Typescript.
I’ve put a working demo of getting some of the basics of an atom package using typescript and sass (sans UI interfacing, which as you mentioned, seems difficult to make work) up here, you might find it useful:
Iterative development with other transpilers (TypeScript, Traceur, JSX, etc.)