Where does it say that?
The apple gate keeping here is terrible.
Or maybe Apple took it down because - as you said - it violated the store guidelines. Or Apple just encouraged them to do it by themselves (for a better PR). So effectively, they were forced.
There is absolutely no information about this time. Actually according to the content it is again Facebook and not Apple who removes the app.
The rules state that Enterprise apps must only be in the hands of users who are under the supervision of the company which operates the Enteprise certificate. It's likely that Apple doesn't consider the people Facebook have co-opted into this program to qualify
1) Facebook said to the media that they’d stop distributing it to iOS users.
2) Apple revoked Facebook’s certificates from the enterprise signing program.