First, have you read http://www.matasano.com/articles/javascript-cryptography/ ?
I hadn't yet seen that particular article but I'm very familiar with those arguments. Thanks for the link! I agree with them that building a crypto library in JS that can be trusted regardless of the security properties of the web application is impossible (content-controlled code, runtime malleability). However, I don't think those points mean that building an application that as a whole has good security properties…
It isn't clear that you are properly taking into account the fact that a browser (also known as a user-friendly Remote Code Execution Engine) is an especially hostile environment.