I think you hit the nail on the head. You mentioned one solution. Another is to have a national corps of NCAA-employed officials rather than people connected with particular conferences. Of course neither of these measures is on the horizon.
Keep in mind also that in the case of Penn State and the Big-10, the issue goes deeper. There was a lot of resentment toward us in the league from Day One...and hell yeah, Ohio State was one of the main offenders in that regard. Even the friggin' Ohio writers hated us.
In fact, their university president, Gordon Gee, reportedly went to the trouble of privately telling some sportswriters' that Paterno was overrated. I mean, you could cut the hostility with a knife, and the message was clear: you may be hot shit in the East but don't think you'll come into this league and ever be on the same plane as Ohio State and Michigan.
A few years in, Joe knew we'd made a mistake joining and broadly hinted at that, but he also knew there was no going back. And all the time the overarching irony is that we rescued their chicken-ass league from the mediocrity and irrelevance to which it had descended after Woody had won his last national championship over 20 years earlier.