He may have. His words have been universally condemned, but also have been somewhat accepted (even subconsciously).
I've noticed that many (not all) top analysts and talking heads (see Kratt...) have discounted the BYU victory over uu. Almost everyone that I've heard has called it a win after a controversial call. Some have even said that BYU should have lost the game. As a result I've seen many talk about putting several 2 loss SEC teams in front of BYU.
Sure, the AD's comments doesn't hurt BYU's record, but it 'taints' the W in the eyes of many. If BYU gets to the B12 championship game and loses, they may not be ranked by the committee high enough to get an at large bid. This means that the B12 is a one bid league. With each game being worth $4MM, excluding one team from the playoff picture is a big deal.
uu is screwing over the conference that extended a lifeline. Maybe $40k wasn't enough of a fine.