The secret inquisittion is committed to protecting society from witchery, using fear and surprise with ruthless efficiency.
Killing a witch would bring tremendous bad luck, but there are other ways to get the job done. After catching a witch the inquisition deliver a humiliating punishment and leave her securely tied up deep in the woods for nature itself to pass final judgment.
The nature spirits will indeed take care of this. Planting superstitions is a well proven method for fairies to get what they want, in this case their favorite: a tied up magical girl.
Plots within plots: This witch already belongs to the pixie Ceding, who is using the inquisition to make contact with the elusive forest fairies.