There is no explicit NFL rule about beating a woman. I get it, stupid, right? Common sense, right? And yet, there isn't. There IS a rule about the proper inflation of a football. And he broke an official NFL rule. And this isn't the first time the Patriots got caught. That is why I said you will hear "integrity of the game" a lot. And you will. And I'm not against the ref being penalized also.
Not sure why this is a surprise to you. It's also why Pete Rose is not in the HOF. Don't with the rules. Apparently though, you can do a lot of other things and it becomes a gray area (see Peterson, A. and Rice, R.).