I sense some wishful thinking here. WA will supplement JS not replace it. You'll have a canvas and that's it, but with the JS interface I can see how some people will try to abuse it.

You can get rid of JS's shortcomings for years now with compilation. That's not really the goal here. What I see here is low level access for raw power. Most of the JS apps don't really need it.

Edit: I take it back. According to this note, I don't see what would stop anyone avoiding JS at all. http://webassembly.org/docs/gc/#webidl-integration