Facebook (or any other organization) can only break Whatsapp E2E encryption if they have the private/public keys of users. And since they own the product, they can introduce a backdoor to leak those keys somehow.
Will researchers notice that?
Probably yes, since it is not very hard to reverse engineer the APK file of android version of Whatsapp and analyze it. Plus, researchers can also analyze incoming and ongoing packets to/from Whatsapp for any weird behavior.
Can Facebook take the risk though?
Probably not! Reputation is what companies are leaning on. There are so many dependent and independent security research institutions that works so hard to make a name of themselves by taking down one of those big names, and don't forget that press and media loves chewing on that.
I can only think of one thing Facebook can use to censor Whatsapp without anyone knowing. When a media file (probably also a long text) gets viral on Whatsapp, Facebook can check who downloaded that specific media file and of course who uploaded it in the first place. The media file resides at Whatsapp servers encrypted, and people only share a link to that encrypted file and the symmetric key used to decrypt it (they share it using E2E encryption), but since it is viral Facebook can easily get a copy of that link and symmetric key when one of the employees receives that media file is his/her phone. They take the link and check who downloaded that link and who uploaded it in the first place!