The basic idea is that implementation-related side-channel attacks, such as timing and power draw, are very hard to exploit remotely. I guess you could write a JavaScript implementation of AES that is so bad that key-dependent multimillisecond jitter can be measured remotely. But it's almost impossible to do it by mistake.

The real problems of JavaScript are it's highly malleable runtime that offers no guarantees, everything is writable. So you need to improve browser support before you can write JavaScript crypto, that's why this is a great project: Google has the ability to change Chrome into a secure end-to-end platform, should they want that.