I think it is important to note that the letter from the president was not in response to the fan behavior towards BYU'S fans, but was really a result of the U of A student section at their own LDS fans.

the most organized anti Mormon chants occurred at half time, as an award for lifetime fan support was being given to a local LDS Stake President, and with one of the largest donors ever in the history of the school, Ira Fulton who is also LDS who was present and who was highly offended.

The apology was more for the LDS Arizona supporters than it was for the BYU fans. That such an apology was even given and deemed necessary should give you an idea of how deplorable the fan behavior was.