I thought about blasting them with ultraviolet, but that leaves them leathery and tough. Good for character but hard to chew. How about just blasting doorknobs (and the like) with UV? How would you mount such a light to reach all the crevices? Well, you could make the knob out of glass and mount the light inside.
But it turns out you need a minutes-long exposure to kill bacteria with UV. And glass blocks it anyway. And even if it didn't, it would still be shining out into the room and eyes of students.
However, I just recently came up with another solution: Ultrasound. So a kid grabs a knob and leaves germs behind. He lets go. A sensor notes this and gives a brief blast of ultrasound, dismembering any organics. The next kid grabs and she doesn't pick up the nasties.
Google says this works, but talks about being immersed in liquid. Maybe that can be worked around. Or a gel coating on the knob. Or fill the school with water and equip the kids with scuba gear.