I guess the most important variable in the short term is how much BYU will get from the BCS as an Indy. If its 100k, then byu will possibly get 30K less on a 850 bowl pay out, if the MWC can keep up its dispersal amount. things could be about even for the next two years.
With all the TV money and the extra home game though, possible small discrepancies in the bowl don't really matter much, and 2014 and beyond could mean more money for BYU. And with all that extra money BYU can recruit twelve cam newtons.