Having BYU in a non-BCS conference with Utah competing in a BCS conference would make for strained relationships at the best, and potentially crucial inequities at worst. If BYU and Utah aren't to remain together in the same league, I think BYU's desire would be to remain on equal footing in terms of status and access. If Utah were in the Pac-12 and BYU in the MWC, greater status and access would belong to the Utes.
The MWC has potential to raise its stature with the addition of Boise State. But if the Big 12 were to remain intact with ten teams, and Utah were to leave for the Pac-10 (12), the loss of the Utes would offset any gain Boise gives the league, and the chances of the MWC gaining an automatic BCS bid without the Utes are slim to none."