If you are doing something that definitely requires E2EE that you are certain works and forces the user on the other end to comply, then maybe I could see your point. You would be in the vast minority of users and it's debatable that your use case is worth gutting the functionality for the majority of users who would benefit from being able to iMessage their Android friends, but you would still have a valid use case. I would tell you in that case to use an open source E2EE solution instead of Apple's closed source one though, given that privacy is such a concern.
The problem is: the client application itself is a big unknown. Beeper says it's secure, and it very well could be. But we have no idea. But if it receives, decrypts, then sends sensitive information, as diagnostics, back to a a central server unencrypted, for example, that's obviously a huge problem.