I was standing up by the rafters between the MUSS and the BYU student section (got there late with friends, no other seats available in the MUSS). I didn't see or hear any behavior like you are describing.
Am I saying nothing happened? Heck no, I saw:
MUSS and ROC members shouting back and forth and flipping each other the bird.
Signs from the BYU section that I found idiotic but accepted because it's part of a rivalry.
Taunting and verbal sparring back and forth, which was fun. I loved the chants "Just Like Football" (Utah), "Bowl Game" (BYU), "Why So Quiet?" (Utah), "BYU" "Sucks" (BYU then Utah), etc...
One guy being a drunken idiot and a pain in the butt right in between the two sections. He was escorted from the premises quite quickly.

But I did not see/hear any bashing of religion. What people don't seem to realize is that a large portion of the MUSS and the Utah fanbase are actually LDS themselves and wouldn't condone that behavior. God, I'm friends with the guys/girls who dressed up as Jesus and the old farm couples for the Holy War and all of them are either LDS or very respectful of the church. Though we all have fun during rivalry games, we all are or at least have friends who are LDS and treat the church appropriately. So, until you can provide me with some proof of this actually happening, I'm going to call bs on this. I'm sorry you didn't have a good experience, but I can't believe that it was as bad as you describe, especially given that I was in that area during the game.