I really don't care that much about a conference championship from the MWC UNLESS it would mean some inclusion into the playoff system. Even the NY6 Bowl games have lost some luster because they are second tier to the playoff.
I'm sure it was cool for Western Michigan to play Wisconsin in the Cotton Bowl last year-- but we play Wisconsin at home this year, along with LSU, Mississippi State, and Utah. We already play the Boise every year, who is probably the only team out of the MWC that really has national cachet.
Independence means more $, more appearances on national t.v., more games against P-5 teams.
It really isn't even a second thought in my mind. Unless the inclusion guidelines change for the playoff, their simply isn't much incentive for BYU to join the MWC.