While I am a bit more optimistic on what the Patriots can gain (greater doubt about Goodell/Wells among the public has its own reward to me) and the chance at Brady's suspension on paper being nearly erased, I largely agree with you. A magic bullet that makes this all better is almost completely unrealistic. The emperor will still be here and the Patriots will always be guilty in the eyes of the putrid but most important jury, goodell and the rest of the NFL Stasi. And making enemies with the NFL exec office is likely to have some, though probably only smallish, level of ripple effect on the team (just is what it is -- they control many things the Patriots have to interact within).
The other benefit not listed regards the NFL going nuclear on the Spygate thing. The Patriots took it without so much as a peep. IMHO it was that acquiescence that helped embolden the NFL exec office to go nuclear again. Gotta set the tone that you better be prepared for outright war if you are going to go nuclear a third time. When people think there will be a war to fought they almost always think twice about going nuclear (what's the old saying? Never strike a man in anger unless you are absolutely sure you can get away with it?).
Getting Brady's suspension all but erased and Goodell/Wells fairness and integrity being impugned by an a third party (an arbitrator, a judge, our own expert reports, any of them) for me will be very satisfying if it can happen (will it? at best maybe). I realize it will be an ugly process and I am not happy about it, however, what the NFL execs did from day 1 of this is appalling up to and including going nuclear on the Patriots and Patriot Nation. I say F 'em! It never ever had to be this but they wanted this way -- so let's give them the nuclear war they started. We are already as dirty as we can get! more dirt means nothing for us but every bit on them will have an effect (just desserts in my book!).