I would love to be able to use the Thunderstorm spell to lay waste to waves of zombies, but I've accidentally had it kill my pets. would it be possible to make it so that you can blacklist specific mobs and animals from getting hit like you can with players?

In wizardry 4.2, you can! Set the friendly fire option to Only players to prevent you from dealing magic damage to pets, or None to prevent you from dealing magic damage to pets and allies.

Thunderstorm may not work completely because it uses vanilla lightning bolts, which don't currently count as wizardry magic damage. I might be able to fix this though.