I think you're conflating villainy with evil. Eboshi abandons her village for cash in the climax of the film. SHe's told the village is in trouble and says "let them deal with it, mama's gotta make that cheddar"

Jigo lays a trap that sacrifices hundreds of his own men in order to kill a god.

I'd put both of them in the villain category. Before the battle, I wouldn't put either of them in that category, but the climax really makes them out to be awful people. Eboshi in particular hides behind smiles and buying up the contracts of prostitutes (to make them her slaves) and helping lepers until the climax when she completely abandons them, throwing them to the wolves in service of money.