I too hated the train noise last time I was at the game, and if a fine and 5th round pick is what it takes to get rid of it I'm not sure I'd be upset.
However, if the league hasn't given "notice" of the fact that a train sound triggered too late can cost a team money and draft picks, then it could be challenged in court. Just make sure that the same judge hears the case.
Also I look forward to the courtroom sketch of Rex Ryan.