D.,
I realize that you're adamant about not sedating your son, but in order to get through the MRI successfully, he has to be EXTREMELY still, and like others have mentioned, if he wakes up halfway through the procedure, it might just cause unnecessary trauma. My boy was 13 months old when he had to have an EEG done where they attach a bunch of wires to the head to measure brain waves, just in case (his daycare provider said he'd had 2 seizures, but we never noticed anything). In our case, they gave him a little vial to drink, and he basically just fell asleep in about 5 minutes. We laid him on the table, they attached a bunch of wires which took about 30 minutes, then ran the EEG for about another 30-45 minutes. Then the nurse began removing the wires and he started coming to. She was able to get all of the wires off before he fully awoke, luckily, but he was fine. He was groggy, almost like he was hungover, but by the time we made it home (30 minutes) he was ready to play again.
It's a scary thing to watch your kid undergo something like that, but without sedating him, you'd just be wasting the doctors and nurse's time, as well as traumatizing your son. I say allow the sedation and let him sleep right through it.