I do find if funny that you hear some probably fake story and it rocks your fandom world. Wow. BYU administrators, students and athletes aren't any more perfect than those at other schools. Mistakes will be made (and if not, some mistakes will be made up by those that hate BYU).
My brother used to go to UU games and cheer them on (he was also a Y fan). He hated how many UU fans acted and treated others at the game. After the TCU game he said that he'd never cheer for them again because of how they were behaving. Oh and he's no puritan in any way.
I grew up in SLC and cheered for all Utah schools — especially BYU. UU fans were crap to me (even when their team was complete garbage). I understand the rivalry aspect of sports and it never bothered me. As UU got the upper hand and fans became more obnoxious, I followed their team less and less — I usually don't know who they are playing or when. The anti-LDS rhetoric hasn't helped me want them to succeed.