I think the NFL handled this pretty well.
The expulsion was the big one, but you can argue that Irvin's fine should have been larger given his role. On the other hand, it was a heated and emotional moment and it had been a clean game up until that point.
Otherwise I think the "pocket change" level of the fines suggests that the NFL isn't all that upset about what Gronk and Hoomanawanui did, but feels that it can't let it go because punches were thrown.
In general, I think the officiating was pretty good and consistent.
They "let them play," as you can see a lot of hand action between defenders and receivers throughout the game that I've seen called during the regular season this year.
Also, each team has a legitimate beef about a couple of calls
Everyone in the announcing booth pointed out that the "Running into the Kicker" call against the Pats should have been "Roughing."
Butler clearly tripped Kearse on the play that's been rerun a few thousand times (and he covered it up like a veteran too!).
Either call could have altered the flow of the game, but the missed Butler call occurred at a more critical time of the game, so the Pats came out a little bit ahead as far as I'm concerned.