You generally want to err on the side of caution with prions. If you infect the patient say with Golden Staph or something like that at least you can treat them but once you "infect" them with prions, there is really not much you can do for them at all. They're pretty much dead at that point, its all down hill from there. As far as i know there's nothing available to treat prion diseases at all. So, even if there's a small chance of infecting someone, tiny chance, its a lot better to just destroy the equipment.
Just to reiterate what i said above, if you infect them with some other disease you can probably treat it but once you "infect" them with prions, they're pretty much more or less done for. So, yeah it might cost a bit to replace the equipment (you wouldn't have to do this often anyway, prion diseases are pretty rare) but it's a lot better than even having a small chance at fatally infecting someone.