I guess it would be possible to accalerate a beam of protons without superconducting magnets or vacuums, but then it would take a lot more energy to get the beam to an accaptable speed. The speed of sound would seem a bit slow, but the beam could exist and go through his face.
But I don't understand how it could have been burned just through one part of his brain, was the beam turned on while he was putting his head in front of it, and then turned of? Because if he would have put his head inside the beam while it was turned on, it would have more like sliced his head right? unless ofcourse the frequency the protons were released was actually very slow, and that only one proton went through his head...