Utah is not playing well right now, but it was good enough to beat a Colorado team that lost to UCLA by 4 after leading late, led USC late before losing by 3, and led Arizona late. Colorado is not good, but they're not horrible.
And if you want to talk about how the teams would fare if they played today (as opposed to the original question of who had the better 9-3, which is a laughable question), while Utah's dinged up, their D has been very good. Based on what BYU's offense did against every good defense it played (and against SJSU as well) I have to believe that there would be a low-scoring game, but BYU would probably have a tough time scoring or stopping Utah's running game.