He broke the law. And for every law there is a punishment affixed, right?
There are the Laws of Man and the Laws of God. Each have their own set of consequences for our actions.
Let the Laws of Man do their job (crappy as they can be, sometimes).
BYU tries (emphasis on TRY) to implement God's Laws as part of criteria to go to school there.
While I am empathetic to his plight. I often don't understand how these things happen. It can lead people to judgement.
What would mercy look like to you, while satisfying the need for justice? Mercy does not rob justice, so there has to be a medium. What does that look like to you?
On a personal note. I feel sorry for the kid. Must be hard to live having gone on a mission for a short time, and not really "getting it" yet. As is evidenced by so many that do these things.