Goodell did punish the Patriots in 2007, a first round pick and $$$.
In my opinion, this is not a serious breaking of the rules. But they will likely get punished anyway.
The NFL should take the punishment duties out of the commissioners office and have a specific person in charge , similar to the NHL.
IF the NFL is so serious about the uniformity of the game balls, why is each team allowed to control the balls all week up until just before the game when the refs check the pressure. And why are they put back in control of the team. Also, why does each offense choose their own game balls and why doesn't the league control it for both teams.
I don't believe the NFL feels this has a huge effect on the game, but they have a poorly written/enforced rule that will likely change for next season.
This is an overblown issue and doesn't greatly alter the outcome of the game.