I'd say the father did it because the guy was a pervertER; he caused the boy's loyalties to change from family to him. The abuse went on for over a year and, apparently, the boy didn't tell his parents. The karate teacher did serious damage to the family arrangement, not just to the child. It was more than molestation or kidnapping, it was loss of security, loss of trust, meddling with thought processes, all kinds of things that will affect them all the rest of their lives. The boy didn't deserve that, his family didn't deserve that. The guy did wrong and knew it, else why the secrecy?
All these things don't have to come up into the conscious mind in order to know how to handle such a situation. All that was necessary was for the father to restore his son's trust. What better way than to eliminate the destroyer?