If WhatsApp uses a version of libsignal whose copyright is solely in the hands of Open Whisper Systems, OWS can have a separate deal with WhatsApp which does not involve the GPL. AFAIK, this is already done to get Signal into the App Store (IANAL though).
Moxie was brought on as a contractor at WhatsApp iirc, the code wasn't just purchased. While WhatsApp uses the same cryptographic architecture its likely they didn't just drop in libsignal (as libsignal is set up to tie into Signal's servers, rather than just be an encryption library like OMEMO or olm).
If your looking to build software that integrates with Signal, then libsignal is great (having built a few things with it).
