With beeper, they are enabling the functionality for android. That is every android user signed up with beeper will end up costing Apple some money to send messages to iphone (or to send messages to other android users using the same thing).
In my opinion, next step for Apple is to mandate having an apple device to be able to use an Apple ID as part of their TnC. They will keep closing loopholes in the meantime, but don't think Apple will let beeper win this, purely because of the can of worms it opens up.