Sounds like all you did was equate losing games to the style of the offense drastically changing. Going from Hill to a more traditional style QB isn't the big issue. The offense can be run just fine and Stewart showed that in numerous games.
What exactly do those games disagree with as far as your style of QB? The defense giving up 41 pts/game was a much bigger problem than BYU's "problem" of scoring 27 ppg. They also had either no Jamaal or a limited Jamaal in all 4 of those.
When you figure for a half game against USU, Stewart was producing 311 total ypg in those 4 games. Plus 2.5 TDs/game. The offense gave every chance to win except against Boise.
The transition to a different style QB is nothing. It does not require a lot of adjustments. Those games don't say anything about it. All they say is that yes, we got a brand new QB on the fly in the middle of the season, in the middle of a game, all while the defense was crapping their pants over and over and over through those games.