Of course Apple doesn’t want others to access the iMessage protocol. It’s part of their walled garden. They can claim it’s a secure protocol because they have full control over it. An application like Beeper gaining access undermines this.

Beeper doesn’t access some sort of global repository of messages, but we’ve no idea what Beeper does with the conversations that are had via their clients. With iMessages you trust Apple, feel about that how you will, with Beeper you trust whoever is in charge of that.

Beeper is never going to last anyway. If they manage to regain access to iMessages, Apple will just update the protocol to reject them again. With Apple implementing RCS there’s not really any point in applying legal pressure on Apple to open up their platform either.