1) BCS automatic qualifier status will not affect BYU's decision. The MWC is not getting BCS AQ status. Yes, the MWC did pick up Boise St, but their pre-MWC accomplishments will not count towards BCS qualification. Without Utah, the MWC doesn't stand a chance. As it stands, BYU needs to be undefeated to be considered for an at-large invitation to a BCS bowl. If they stay in the MWC, BYU will need to be undefeated to be considered for an at-large invitation. As an independent, BYU will need to be undefeated to be considered for an at-large invitation.
2) BYU averaged 64,000 at home games and has a relatively large national fan base compared to most schools of its size. The MWC average a little more than half that. Fresno St and Nevada, together, would only bring that average down. And the MWC tv deal is terrible. Without Utah, what incentive, financial or otherwise, does BYU have to stay in the MWC?
3) Why does BYU want to leave? Exposure. BYU has a slight divide between those who support the football team for the sake of the football and those who think that the football team should only exist to serve the broader mission of the university and the Church that owns it. Exposure brings both sides into the same camp. That is why independence will happen.
4) Why else does BYU want to leave? The MWC is now tainted with the stench of the conference that Utah left behind. To retain standing in the rivalry, BYU had to make a move. BYU is trying to regain pride by becoming the Notre Dame of the West.
5) Independence will not be a financial move. The raison d'etre of BYU-TV is to be seen, not to make money - that is why it has state of the art equipment to broadcast devotionals. BYU would have to jack up the price on BYU-TV to make money from televising football games. BYU does not want to jack up the price. They want to retain 100 million subscribers and potential viewers (exposure!).
In sum, BYU's BCS status will not change. BYU will not make more money as an independent (but they will not make less), but they will gain exposure. Everyone is happy, for now, in Provo, and BYU can claim some kinship with Notre dame, Army and Navy when Utah clamors on about the Pac 10.