Personal conduct policy says you can be suspended for behavior detrimental to the image of the league, its teams or its players. Basically it outlaws generating bad press. Most of the players suspended under it were for legal troubles that never resulted in charges much less guilty verdicts.
I don’t think Brady generated any of this press at all. The Colts generated it.
Unless they can prove to me that Brady let the air out of the balls or ordered someone else to do it, why should I believe he did that?