You have to analyze the threat model. Take the note taking webapp they use as an example. Without javascript crypto, anyone who breaks into the server can read everyones notes. Likewise, the FBI can get a warrant and have the owner of the web application turn over everyones notes.
If they do use javascript crypto, instead of just getting a warrant for the machine, the fbi has to convince the owner of the site to modify their source code to target an individual user to steal their key. That is a significant difference. Also, the victim user has to log in again for that attack to be successful, if they just used the server for a couple weeks and left, they are safe.
Likewise, an attacker who breaks into the server can't get a dump of all the notes in the system. They again have to modify the source code which could be noticed by the owners and users and takes some level of sophistication more than the average aim and shoot attacker
So is javascript security perfect right now? no... but that doesn't mean it should be dismissed