Van Noy could have chosen to forego the suspension and attend some state school instead. But he wanted to attend BYU which required something more in response to his mistake.
I may disagree with the actions and decisions of DAs and judges but ultimately it is they who hold the place of civil judgement. It doesn't need to be the University, the football coach, or the AD who ensures civil punishment. They may deem other punishments to be necessary to preserve a certain atmosphere balanced with the desire to win but even that isn't so cut and dry.