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"
replyJigo 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.
She has made a somewhat Faustian bargain with the other warlords and by extension the emperor. She is very different than them in caring for outcasts, but the state is still the source of her power, so when the emperor wants the deer-god's head she goes hunting, thinking quite naturally that this is the best she can do for her outcast villagers. Money for the village's needs (they are far from self-sufficient), the emperor's favor, and (as far as she knows) an end to god-attacks on the village? Of course she goes. The villagers are equipped to deal with more short-term threats, she made sure of that.
replyShe is absolutely a non-evil, non-villainous antagonist.