The fact of the matter is, especially when Thomas went out of the game, it was extremely obvious Oregon was going to strictly run the ball, I don't know how you can deny that. The defense made no adjustments whatsoever, the CB's were still 10 yards off the LOS, and the safeties were 15 yards away, as if they're playing the deep ball. Regardless of the CB's covering skills, when a Freshman QB enters the game, you should immediately take away their best asset, the run game.
By putting 8-9 guys in the box, and playing the WR's man to man, you are limiting Oregon's run game. I'd much rather have a freshman try to beat me through the air than just running it over and over for 20 yards a piece, it doesn't make any sense. It's inexcusible to let them run for over 250+ yards and never make a single adjustment to stop the run game. Also, I'm not sure if you noticed, but Oregon only threw the ball a handful of times in the 2nd half, so common sense would tell you the CB's should be on the line for run support. Bray really put this defense in a losing situation by calling such a horrible vanilla defense, there's no way you can deny that.