Actually, we do have a historical model for this: witchcraft. Whether or not you believe in magic in the real world, women (usually women) were perceived as having powers that men couldn't usually understand, and were reviled for it-- it was called unnatural and against God. Those few men who also were rumored to have the powers were also considered ungodly, although interestingly I never heard of them being called womanly. I think superpowers would also constitute an offense against the Church if they started up in the 1800s... you could even postulate a world in which superpowers basically WERE the "witchcraft" that these people were accused of.