I totally agree with the overall message of your post. Winning trumps everything, and for that, Sitake, Arod, and Retzlaff all deserve serious respect for the season. That said, I don't think addressing blunders (by players or coaches) or implying that there might be a more creative/consistent OC out there for BYU is the same as saying, "I could call a better game than ARod." Obviously, any noncoach who believes that is delusional to some degree.
I'm a true believer in the idea that great programs have to constantly take a hard look in the mirror, even when things are going well. Even though we are 9-1, there have been severe, embarrassing mistakes made—the kind of mistakes that sully our brand and worm their way into the heads of the CFP committee.
Do I think we should fire Arod/Sitake or bench Jake? Absolutely not. As you said above, that would be borderline insane given our season. But I do think that when the season is over, all the mistakes from the season should be reviewed and addressed as part of any decision-making process, whether we end up 9-4 or go deep into the playoffs.