I don't know that byu staying in the mwc is a better option than independence, you're assuming boise wouldn't have gone to the big east. byu is after exposure, and they are on espn quite a bit, which is really what they're after and the mwc didn't offer a lot before the better football teams left.
In hindsight, I'm positive BYU/BSU/SDSU would all have been better off staying together and limiting their MWC membership to Nevada, Hawaii, Fresno State and previous MWC schools. There's no scenario where TCU/Utah would have been wise to stay but the way things shook out the other three made the wrong choice.
At the time the decisions were made I understand the choices of all 3, but it really f'd things up for themselves and the whole FBS conference picture.
The unfortunate thing is that the choice that would have been best for those 3 schools in hindsight, would have also majorly helped nearly a dozen other schools, a few conferences, and college football as a whole.
BYU is going to be stuck scheduling nobodies every oct/nov. They could have scheduled powerhouse teams early and still had BSU, Nevada, Hawaii on the schedule later. Not a B12 schedule but much better than their option now.
BSU and SDSU aren't going to hang onto the AQ bid they sought because AQ is going out the window. SDSU was never going to get it over Boise State anyway. They aren't going to play any regional conference games, and their SOS is going to be exactly the same as it would have been if BYU/BSU had stuck it out in the MWC together.
College football landscape as a whole would have been better off with the Big East adding just 3 teams from among Navy/CUSA to get to 8 until they get raided again, not the 7 they added to their remaining 5. When UConn, Rutgers and Louisville left it would have been a zero big deal for Cincy and USF to go back to CUSA where they came from, especially now that there's no AQ. Instead we have this monstrosity of a conference that makes no sense.