Boise State is not running up scores. They had their backups in at that point, and they're going against a D-I school, who also have scholarship players and are in the same division. Kellen Moore and Doug Martin were not in the game at that point.
In quarters 1-3, Boise State are outscoring their opponents 34-6. In the 4th quarter, they are being outscored 9-7 because they take their foot off the gas and have their 2nd/3rd stringers in. If Boise actually wanted to run up the score, they would be blowing out opponents by a lot more than they are.