If someone were to set up a website that reviewed games and rated both calls and egregious non calls, it would put the NFL on notice. The different ref groups would then get a rating. Kind of like PFF does with stats, but for refs. This could be an independent source that could be referenced by talking heads and sports news outlets and would force the NFL to really look at and punish poor calls.
As far as the NFL actively taking part in telling refs how to decide games, I do not buy it. All it would take is one whistleblower to take down the entire NFL empire. I think it is more than likely individual refs that have outside motivations. Possibly monetary, maybe just personal.
One thing is for sure, this was one of those rare games where it was apparent that it was not officiated fairly and consistently. They will not change unless they are forced to. The public outcry and loss of revenue is the only thing that will force that change. NFL is about dollars not integrity.