Okay, as quickly as this happened and as closed mouthed as Bohl can be (which is good), I have a theory on this...(If I"m full of crap, just say so..)
Bohl went to Smith in Oregon, told him that things are going to change in the offense. Smith decided to leave early for the draft.
Bohl went to Thompson and told him he's welcome to stay, but again, things are going to change and he's bringing in a Juco that he will have to compete with for the starting position.
Thompson left for Utah rather than be subjected to the "humiliation" of competition and probably loss of the starting position to this Juco guy who would fit the new system much better anyway...