How could this possibly be upheld?
My gut feeling agrees with you, however, the law isn't about fairness or what's 'simply right'. The law is a bunch of paragraphs of specifications (or the lack of paragraphs). The judge could say ' RG can arbitrarily decide guilt and punishment under Article 46. That is what the NFLPA agreed to...case dismissed'. I don't expect (or hope) it will not happen but it could. Yet it has a tangible chance of happening regardless of how unseemly and dishonest RG has acted.
At this point my disgust will begin to point more and more to the NFL owners (and I hope the sucky media gets on this reality too). The NFL owners enable Roger Goodell, a man who is a confirmed liar and is motivated by the ugliest 'the ends justifies the means'. There is no arguing or denying this fact. Whether Brady wanted a football deflated is no longer an issue connected to this (it is a separate issue altogether). Roger Goodell is a calculated liar. When he wants a result such as harming someone's reputation/livelihood, he will get up on a podium, speak into the microphone and he spread calculated lies in order to hurt someone. He got up in front of hundreds of thousands if not millions of people to tell them 'we decided person X is a cheater and cannot work in my league for one month because Ted Wells, who is a fair and completely independent man, says Brady is a cheater' (and again saying it to hundreds of thousands/millions of people). We know this was a planned and calculated lie, there is no gray area on it. Clearly nothing is more important than getting his way/whatever result he wants no matter the cost or the lies. Again, this description of Goodell is not patriot homer glasses, this is fact. It isn't open for interpretation any longer, there isn't any gray area. And all of the owners absolutely know that the public knows how Roger Goodell operates.
The leader of the globe's premier sports league, the NFL, has demonstrated an ugly level of ethics/how he operates. His behavior would probably cross criminal lines if not for the CBA. So if the NFL owners allow this to go unpunished then they are just as responsible and just as lacking in decency as Goodell. And any damage to their league will be richly deserved for not doing anything about it, for not making a statement about what the league stands for.
((I don't expect the owners to do anything right now. It would be bad business to punish Roger Goodell in mid litigation. But when it is over they better make a statement through their actions that says their league will not operate without an acceptable level of ethics))