My guess is that they will hammer Baylor fairly hard because in the total scheme of things they aren’t “athletic nobody”.
Now if it was one of the big schools or “legacy schools“, like Alabama Texas, etc, your hands would be spanked and the NCAA Would say something like “don’t ever do that again”.
I think they're done trying to hammer P5 schools for 2 reasons.
1) They tried to hammer Sandusky U and it backfired hard.
2) They're worried about the cash cow breaking away and starting its own governing body where money can flow more freely so they won't dare do anything to upset the apple cart.
You may be right in that Baylor could potentially be left on the outside looking in if the P5 reorganizes outside of the NCAA, but I think they'd find a way to stay involved and I think the NCAA is too gun-shy after PSU to truly hammer anyone other than Boise.