Why would they need to look into Apple's conduct here? Investigate Beeper for CFAA violations since they cracked into Apple's internal APIs and ignored large chunks of their ToS in the process.
Of course Apple is going to shut down unauthorized access to their messaging system. They'd lose all customer trust instantly if they didn't.
ToS have almost universally been shown to be unenforceable in court. I'm also not sure what the hell you mean by customers would lose trust. It's not as if they had access to information they shouldn't, all they did was reverse engineer the protocol. They still had to have an account and a login and they still only had access to the data that account should have. There's nothing to lose trust over the only thing beeper was doing was emulating being an iMessage client