Boone was left in a kind of coma. His level of recovery is open to anyone who wants to NPC him. The Doctor fished him out of his self imposed exile in his own mind, and de-programed him as much as he could in one session. He might react to a preprogrammed trigger, but he will be able to fight it and have some control over himself.

However, whatever damage Ami was forced to do has to be worked through yet.

He is bound to a bed with medical restraints, and his burns have been treated. Of course if he isn't found, he may starve to death or wallow in his own elimination.

My aren't I cheery...