Exceptions can be made for many reasons, in Jimmy Mac's case I think it should have been made because there are probably less than 5 people who have done as much good for BYU football as he has. His success on the field did huge things for BYU. And you should be able to understand that reasoning, you may not agree with it, but it's pretty easy to understand.
Yes,they should have looked the other way, either enforce your standards with him or don't, it wasn't until after his last football game that they chose to enforce anything.