When a judge says "please do this" you need to take it as "you damn well better do this".
But now that Goodell has upped the rhetoric to insist that Tom was a blatant cheater who also offered bribes to cover it up, I'm not sure that Tom will even accept a significant fine. If they explain that to the judge, he may be sympathetic.
The judge isn't trying to get himself off the hook, he's just trying to end this once and for all. A settlement ends it. A ruling may not, as it may just send it to an arbitrator if he sides with Tom. If the NFL won, it would be over though. God that would suck.