Thanks to the Fifth Amendment, nobody is obligated to plead guilty at an arraignment.
I imagine that his lawyer will try to negotiate a plea, at which point he'll withdraw the not guilty plea and enter a plea of guilty. It happens all the time.
I had a somewhat similar case happen to me. I was living off-campus in a college town with a roommate who absolutely refused to lock the door. One night, I came home from my night job to see a drunk man passed out on our couch.
It turned out he had wandered in, mistaking our place for another on the same block, and my roomie's idiotic refusal to lock the door led to the whole situation. I didn't want to call the cops on the guy, so I tried waking him up, but he was too far gone. So instead I found his address, picked him up in a fireman's lift, and carried him to the house down the road and handed him over to his roommates. Now he was their problem.