I think you guys are reading too much into this, as well as confusing things a bit.
It is acknowledged that the instant replay protocols were not properly followed. This is magnified by the improper procedure taking place at the very end of the game, and the outcome of the game would have been different if the correct protocol was followed.
But the incorrect following of protocols is really not any different than a ref missing a penalty that should have been called, on a play that resulted in a score. Or a ref incorrectly ruling a ball was a catch when it had hit the turf, or vice-versa, on the last drive of a game (especially on 4th down).
I'm not involved in college football officiating or league administration, or the same things at the high school level. However, I am involved in those things for a few other sports. And in each of these sports, there are either competition rules, or league rules, or state rules, etc. that specify that the decisions of the officials on the field are final. I know of situations where a rule was improperly applied at the end of the game that decided which team advanced to the state playoffs, and an appeal was made, and the governing body in so many words said we're sorry about what happened to you, and a mistake was made, but the decision made on the field by the official(s) is final, and can't be overturned, or re-played.
I'm certainly not a fan of Michigan. And for once, I would like to see them treated properly by officials, or the B1G, or be properly punished for illegal actions. But I fully expected that nothing would come of the appeal filed by the MAC, as I was pretty certain there was no mechanism to change the outcome after the game was played to completion.