I watch a lot of Boise football (they're my adopted team) and for me and seemingly a large chunk of the fanbase the writing is on the wall: he's leaving, just a matter of where and when.
Going into this season they randomly and arbitrarily completely switched offenses away from Pete's shift-and-motion to a traditional type spread and all the plays were called by the OC (as opposed to Pete having a large say in the past). That speaks volumes to me. Just watching the games too, he was seemingly way less involved this season.
I honestly think part of the reason he didn't leave was his relationship with Kellen Moore and also the fact that BSU had a legitimate crack at sneaking into a few BCS bowls if not the championship game (if they had a kicker).