BYU remaining in (and perhaps dominating) the MWC would have been, in my opinion, a better outcome than BYU wandering in the wilderness for more than a decade, trying to pretend that they were P5—especially for MBB and the non-revenue sports.
I'm also not convinced that BYU's entry into the Big XII was aided in any significant way by their independent status—BYU was the best brand left, and that would have been true if they were in the MWC, the AAC, or an independent (it certainly wasn't a problem for Cincy, UCF, and Houston to leave their conference).
As for the "but the money was better" crowd—I think it's a fool's bargain to trade wins for money.