I get your rationale (more, better wins, etc.), but I was at the game and Boise flat out dominated Oregon. Oregon had a single productive drive and rarely even made it into Boise territory whereas the BSU offense moved the ball all day against the Pac-10's best defense. While their offense was better against Oregon that anyone else I saw this year, what stood out was how good their defense was, something you don't normally see in mid-major schools. I honestly can't remember the last time a top 10 offense nationally got shut down that thoroughly for an entire 60 mins (to the tune of two turnovers and 150 total yards and 31 yards rushing, almost all of which came on one drive to open the 2nd half).
If it was a close game where either team could have won I can see jumping Oregon over Boise, but it wasn't: the Ducks were physically man-handled on both sides of the ball.