Ouch, that's a great point about versioning.
The thing that appeals to me about asm.js is that it short-cuts the long, slow path of VM optimization and gives great performance now instead of five years down the road. Sure it's an ugly hack but that doesn't matter to your users, all they see is a much faster user experience.
Now all we need is a SIMD API for JS and we can write some truly amazing apps.