The thing of it is, the commissioner's power of discipline has become this super high profile piece of the CBA, one that will definitely be focused on by the media in the next renegotiation. It works in the league's favor, because on the grand scale, it's a tiny thing. It directly affects a ridiculously small percentage of the union's members, but because of how high profile its been, if a new CBA is agreed upon without having it changed, it will be viewed as a loss for the union. The league is going to use it as a bargaining chip to get something important from the players. You can count on it. And what would the league really lose if they gave up some of the commissioner's power? Like, if they went to neutral arbitration instead of it being under the commissioner's power. Not much loss there. Yeah, Brady might not have been suspended, but does that really hurt the league any?
The pressure is definitely on the union to change a system that the league probably doesn't have a huge problem with changing anyway, but they'll make sure they get something for it.