The Big 12 needed schools... pretty badly. TCU was a last gasp, and the Big 12 knew they would come at a moment's notice. I'm guessing that they would have liked to have BYU and probably relented on a number of things, but BYU would hardly give an inch.
If these were religion related (keep in mind this isn't the Pac-12 we're talking about here), that's fine... independence is perfect for BYU. They should run with it.