If his teeth are really impacted, then I would recommend anesthesia. What really stands out to me is his anxiety. If he's already had a difficult time with MRI he might do better being sedated. It's not a super pleasant procedure, so sounds or sensations may make him really anxious.

My DS just had his remaining teeth pulled and they were deep and difficult to remove. He's got a pretty high pain tolerance, but he was in agony within a short time afterwards. Definitely get those pain meds ASAP just in case he's in pain.