The "witches" weren't persecuted for being "witches." They were persecuted for being marginalized/vulnerable in societies that were undergoing massive, chaotic transformations, with populists and mobs who were looking for someone to blame.
"Cunning folk" and "wise women/men" were often persecuted for being at the rural edge of societies that were moving away from the traditional, decentralized agrarian order. They often went to their deaths saying Christian prayers.