The only case that obfuscating code from the user is useful for is DRM. That's not what end-to-end encryption is about. End-to-end encryption is about allowing two users to send messages to each other using keys of users that each user owns on their own device, so no server in the middle can eavesdrop. That use-case isn't impacted by each user being able to reverse-engineer the code they're running. It's probably better if the code they're running is open-source so they can possibly verify it or get someone else to verify it for them.