If they're willing to prosecute some kid who wasn't even trying to make a profit off of his access to a web server, why wouldn't they prosecute a company for trying to sell hacked access to someone else's servers?
Also, there have been many prosecutions under this law. Aaron's case is just the most infamous example.
Beeper is trying to use an api to send message to users. They are not getting nor trying to get shell access to apple servers.
Beeper intent is to serve both Apple customers and non Apple customers to exchange messages securely. Its goal is interoperability, not stealing, or blindly using resources it doesn't own.
The intent is to sell hacked access to somebody else's servers.
If I sell hacked access to Microsoft's Office 365 servers, I can claim to have any motivations I like. It's still a crime.
There are many instances of "adversarial interoperability" (somebody else already mentioned screen scraping of online banking for budget management tools already in a different thread), and I haven't seen the CFAA being thrown at the responsible parties all that often.
I'd be quite curious to see precedent being set here, but I doubt it'll happen. Apple has much more to lose than to gain from that:
They can play cat and mouse on the tech side as long as they want, but with all the attention and scrutiny of a lawsuit, I could see a small chance of Apple ending up having to open up their service for interoperability.