I'm having trouble envisioning how you could possibly put together a solution where the encryption key wouldn't be visible to Javascript, malicious or otherwise. How would that work?
Assuming that the client is essentially a web app then yes, the javascript must be able to read the encryption key.
However, it's not a hard requirement that the server delivers the javascript to us: it could be hosted locally, e.g. a trusted Electron wrapper around a set of HTML/CSS/JS stored on my computer, for some definition of trusted.
This is how a lot of other e2e-encrypted messaging app can be used, e.g. Signal, WhatsApp, Riot.im: a "trusted" set of client code over which the untrusted server has no control.
