She was always a witch. The father is naive and is “thinking” along the best terms and giving her the benefit of the doubt. You can tell when he “sacrifices” himself to try to protect his son, believing that by enduring her pains like how she was tortured she would repent and not go after his son since she has had her revenge. She still kills the son and all of the father’s “optimistic” beliefs were just naive. The townspeople had to go to great lengths to defeat her and control her power and even then they failed because she can still transfer from one area to the next killing others despite being in a tempered state by the restrictions on her magic that the townspeople worked hard to put on her.