The CBA says the penalty for tampering with equipment (including game balls) is a $50K fine. If the commissioner would have fined him that amount, this whole controversy would have been averted. But because he had an ulterior motive, it's now too late to fine Brady.
If the commissioner had any integrity, he would not appeal. But, Roger has a history of making these arbitrary decisions, like suspending QB coach Wade Wilson 5 games and fining him $100K for taking medication related to his diabetes (on charges of using performance enhancing substances...AS A COACH!!), versus suspending Ray Rice on DV charges for only two games (only after the video was released), then changing it to whatever wound up happening with that situation.
There is no doubt in my mind Brady and the Pats used to cheat, are cheating, and will continue to cheat. But the Commissioner is just as wrong, more so really, as he should set the corporate example for personal integrity and conduct.