I believe it is a violation of the by-laws. Kraft really had no choice. I am not going to read too much into comments about how he reluctantly accepted the penalty. After speaking out as loudly as he did, he had no choice but to say, I don't agree with the penalties, but I'll accept them. He was never going to agree with them at this point. If you believe his motivation was to protect the league and the game, then he did the right thing. If you believe he did it because he had nowhere else to go but court, he still did the right thing. Both are valid reasons for putting an end to this nonsense.
The Brady appeal, I do think it will be reduced somewhat. Whether this plays a role in that, I don't know. I never thought Brady would get more than 2 games, so I think that is where they wind up. Then, if the NFLPA wants to make a federal case out of it they are just being petty. If the appeal is denied, then there was probably enough evidence to justify the 4 games in my opinion. In which case, taking it to court could be like throwing gasoline on a fire because a lot more information could become discoverable, and that might not be a good thing for any party.