I would love end-to-end encryption in real time chat!
But here’s the thing: encryption for private messages drastically reduces the uses for those messages.
It isn’t always obvious at first. You can add and remove people from private messages, you can use them in your editorial workflow (I use them to capture notes, before sharing them more broadly!), all kinds of things. Encrypt them and suddenly a lot of what we can do is not longer appropriate, given the nature of the encryption involved.
Okay, so now apply that to real time chat.
Uh oh! We are suddenly going to lose a lot of not only what makes a chat channel interesting, but we’re also going to lose what makes Discourse chat interesting: advanced features that are developing as we figure out how to integrate chat into the knowledge capture processes folks already use Discourse for; adding encryption to that will drastically reduce the usefulness of chat, in this case.
I’m a supporter of encrypt-all-the-things! I use OMEMO for all my personal chats, on a server I control. But there are trade-offs, and they are not what I’d want to apply to Discourse Chat. What we’ve got is going to be something very cool on its own. 
Also, encrypted PMs are like, already real time chat channels, so there’s that!