Several thoughts on this. First, BYU has a much larger stadium than Utah (64,000 vs 45,000) and yet was left out of PAC 10 discussions--that had to hurt. With Utah leaving that left only TCU with any serious BCS bowl hopes. Bringing in Boise with their small stadium did not add anything long term to MWC.
Why not go independant? How many BCS bowls has BYU been to in the past ten years? They can now at least play several BCS teams each year and if they win those would enhance their chances of being a player. They have nothing to lose.
What of the MWC now? With Utah and BYU gone I would think TCU is looking around for options, like the newest Big 12-2 member.