The medieval inquisition was indeed a witch hunt in the figurative sense but it did not hunt witches. It was primary occupied with hunting heretics (particularly Cathars). Its involvement in hunting witches started in the late 15th century at the very end of the middle ages.

I think he was using "witch hunt" in a generic term like we use it today.

Well, in that case the analogy is virtually meaningless, since "witch hunts" have always occurred.