As an Apple customer, I applaud their tenacity. Every time Beeper's protocol hacks are fixed, Messages gets more secure.
By what metric? Arguably, users are less secure since "fixing" Messages (i.e. breaking Beeper) means Apple and Android users lose a secure communication channel. Beeper isn't "hacking" Messages... they've implemented the protocol.
Reverse-engineering a closed protocol and distributing an Apple Binary (IIRC correctly) are a bit more than just "implementing a protocol."