Indeed, hence the sticky philosophical puzzler. I would think that the clerics themselves would start getting affected by the spell. Fortunately (for them), the effect of the spell when cast on someone of the same level as yourself is only deafness for 1d4 rounds. The Church could probably cover that up.

There was another interesting related situation that came up in an actual campaign I was in, involving the Blasphemy spell (a variant that only kills non-evil targets). My party and I were in our "home base", a mansion belonging to an allied NPC noblewoman, planning out our next excursion. A powerful demon we'd been tangling with attempted to scry-and-fry us, teleporting in and nuking us with Blasphemy. Unfortunately there were a lot of low-level NPC staff working in the noblewoman's household and the spell wiped them out instantly... except for one guy, who happened to be of evil alignment. He survived the encounter because of that.

Even though his alignment was evil, though, he'd never done anything wrong and didn't seem like he had any reason to do anything wrong in the future. So we weren't sure if we should fire him or what. It wasn't illegal to simply be evil, you had to actually do something evil before you could be punished. We just warned him we'd be keeping an eye on him, in the end, and kept him on staff.