The argument of having the academies in the conference to preserve the AQ status is absurd. It will have no bearing on it and in fact may push it the other way. Yes, an academy wins a game against a traditional "power" every now and again, but it's hardly consistent (seriously the last time the academies were a consistent threat was when Fisher DeBerry was coaching and Dee Dowis was QBing Air Force and I think Navy got into the top 25 sometime in the past decade).
I think that the BCS absolutely shudders of the possibility of an academy somehow winning an AQ conference championship and getting a bid and playing Oklahoma, Alabama, etc. We got hammered in the court of popular opinion last year (rightly or wrongly), imagine what the academy would get and the BCS doesn't want that to happen. They have a vested interest in driving eyeballs to TV sets and creating ad sales opportunities for their media partners, or partner (ESPN), having what is likely a multiple loss service academy (I say multiple loss because there is no recent history of an academy going undefeated) play a no loss or a one loss traditional power is a nightmare scenario (even with the patriotic sentiments that would naturally occur).