You can't roll your own TLS replacement using Javascript, because you need some way to deliver that Javascript to the browser in the first place. If you don't use TLS for that, you're doomed. Sure.

On the other hand, that's a pretty narrow definition of "Javascript Cryptography". The article overlooks a bunch of other useful cryptographic things you can do in the browser, like end-to-end encrypted messaging. You can't lose a giant database of customer data if you don't have a giant database of customer data sitting around. Javascript can encrypt stuff before it even leaves the browser.

If you build your service this way, an attacker would have to carry out an active attack that injects bad code into your Javascript bundle. That's much harder than stealing a database, and even if it works, it can only compromises the users who log in during the breach.

So, no, the right kind of Javascript Cryptography is actually quite beneficial.