BYU is closely allied with Notre Dame...a lot more than I think most of us realize. Notre Dame likes us being in the WCC. We fill their gyms and get them bigger TV contracts because of our much larger fan base. Therefore because of BYU the Catholic schools in the WCC make more money now. Notre Dame is the big brother for all the Jesuits schools and likes to look over there flock. Notre Dame has a vested interest in us being happy with the WCC.
If BYU suddenly feels that they can move to another conference like the Big East now or the Big 12 in the future Notre Dame may want to step in and convince us to stay. For the time being they've given us a lop sided scheduling deal. However that can be sweetened by negotiating for us to move Football only into the Big 12 sooner rather than later in exchange that we keep our fan base in the WCC.
Notre Dame calls the shots and probably nudged us into independence at the same time landing us in the WCC, but we have a little control and leverage as well.