In the middle-ages, green eyes were often seen as a sign of witchcraft and malevolence. This explains why many early Disney Villains had green eyes.

However, Esmeralda from The Hunchback Of Notre Dame was also designed with green eyes; which explains why Frollo (a man of the church) sees Esmeralda as a witch and intends to burn her at the stake, but knows it's sinful when he begins to have sexual attractions to a supposed "witch".