Trepanation is not the same as drilling a hole into someone's head. It also wasn't just used to release spirits.
The reason it remained a widely practiced medical procedure for centuries is because it is an effective, scientifically proven treatment. It's still common practice to remove part of the skull to relieve pressure on the brain from illness or injury.
A small area of the skull is scraped away, usually with a sharp stone; as technology improved, doctors in richer countries began using "drills", but never to pierce the brain and not the kind of drill the unsub used.