Both are totalitarian systems. Which is better/worse, solidarity in violence or the Koran? The military-industrial complex or the Salem witch trials? Marching in style or Biblical terror?
Anywho, my gut reaction is theocracy. At least under that there's a guide to how the state will act (bible/koran/whatever). Under facism there's none of that, and i don't really want to know what'll happen when the jews, ethnics & gays have all gone. Will they kill everyone else off? At least a theocracy saves anyone who says they're a christian