This is the portion I found most crucial in what you wrote. If it's true that Snyder has influence and dirt on Goodell and the other owners, then yeah they'll look the other way. Gruden was comfortable enough to send those messages. We don't know how Allen responded but if those messages were a pattern, then they were either like-minded or equally unprofessional. Translation: there's likely more dirt. But we won't know that until the situation plays out. There are about 650,000 emails so odds that Gruden is the only bad apple are low.I think Dan Snyder has developed a small, but sufficient amount of clout with his fellow owners. This is all that matters, not that minority owners disliked his stewardship of the the team and tried to buy him out. The NFL ownership does not want to see one of their flock toppled by the Commissioner, because it will only invite scrutiny of their own glass houses (Snyder likely also has dirt on all of them, and Goodell, that needs to be left in the ground).
As for your point about NFL owners not taking too kindly to forcing out one of their own, if the PR nightmare is bad enough the NFL will protect the NFL. The main impetus that causes the league to do anything is bad publicity or the fear of it. As I previously mentioned, if something akin to the Donald Sterling comments happened in the NFL, Goodell will act (assuming his hands aren't dirty too) . You've also seen how the NFL sat on the Ray Rice tape, but Rice was only cut after the media got hold of the tape. Then there was that Giants kicker who admitted domestic violence (years after Ray Rice!) but wasn't released until it surfaced in the media while the kicker had reported to training camp.
The NFL only cares about what's good for business. It's why a silent anthem protest is more harmful in NFL "morality" than all the wife beaters in the league well before Ray Rice. Hell, Donte Stallworth and Josh Brent killed people (DUIs) and still played a few games after serving time. But more fuss was raised about a guy clumsily protesting police brutality, so of course he had to go over people who behaved worse.