Hm. Yep, that is a problem. Maybe we could add an alignment clause: If the two players chosen by the Brain Surgeon don't share an alignment, the Brain Surgeon dies instead. Or maybe the Brain Surgeon always dies after performing surgery. I dunno. We'll think of something.
n1: Hi guys. Im nilla Im jan Im guiser. Who do we kill. Lets kill this guy. d1: (mafia got swapped as town) Hey guys. Ive been swapped. Im town now. Looking at last nights meeting... The mafia are x and y. Brain surgeon: z is the 3rd mafia because I swapped him with you. GAME OVER