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Witch hunts were primarily a phenomenon of the early modern period, not the middle ages, during which both the political authorities and the Church repeatedly cautioned against blaming e.g poor crops on supposed witches.

Also, I believe about half of witchcraft trials ended in execution - I'm not sure what the comparable rate is for Gitmo (although obviously there are no trials).

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Perhaps witch hunts were just performed under a different name. See also:

the Medieval Inquisition (1184–16th century)

the Spanish Inquisition (1478–1834)

the Portuguese Inquisition (1536–1821)

the Roman Inquisition (1542 – c. 1860)

[1] http://en.wikipedia.org/wiki/Inquisition

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.

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