The best time for the NFL to "end this" was early May of last year, with a more honest version of the Wells report. They could have crafted it so everyone got a little positive and negative. First and foremost, they could have said there was no manual deflation and the PSI change was entirely to the weather and temperature changes.
For the Patriots, the league could have levied a penalty similar to what the Falcons received for pumping in crowd noise, a $35ok fine and the loss of a 2016 fifth round pick. They could have justified this by McNally leaving with the balls alone and stopping in the bathroom and by Brady not surrendering his phone. It would be a hit, but nothing crazy.
For the league itself, they could have come close to the apology that Kraft wanted by sacking the people who leaked false information to the media after the AFCCG and sent incorrect information to the Patriots. They could have admitted their ignorance of the IGL and their errors in handling the situation prior to the game. That is, they should have notified the Patriots of the complaint before the game and then had a detailed plan to test the balls at halftime and after the game. This could segue into their new protocols for securing and monitoring footballs during the next season. They would have looked proactive and smart - "We had a complaint, we addressed and found no wrongdoing, and we set up a system to prevent any such incidents in the future."
Finally, they could have fined the Colts $200k for making baseless accusations against another team and for breaking the rules by gauging a football on the sidelines during the game.
That would have ended it. No suspensions, no court cases, nothing lingering into the 2015 season. The NFL had 3 months to come up with a solution like that, but opted to portray themselves as being pure and blameless while nuking the Patriots instead.
Either the NFL didn't see "this nonsense" coming when they chose their path or they did and they decided to proceed anyway. Either way, it doesn't paint them in a positive light. It's also a pretty strong indication that they aren't going to end things any time soon.