Agreed. If it stored data on a different server (allowed via CORS) then there could be some additional security, since then as a long as the JavaScript isn't subverted on the same site, you're storing encrypted data on a different server.

But yes, if you run JavaScript, you're always trusting that site to not do a "quiet update" of the code to something malicious. I don't see any obvious way to counter that, short of downloading the JavaScript code & running it yourself.