While I can understand the motivation of those beginning the Inquisition, and also understand that they lived in more savage times than we (at least here in the US - I wouldn’t say that about much of the Arab World), the gratuitous use of the most horrible forms of torture by the Inquisitors over the course of centuries, and even in the New World, wasn’t justified. Torqueamada didn’t get his brutal reputation for being a nice guy. Burning people alive wasn’t excusable, and it was done a LOT. Check out http://www.jewishvirtuallibrary.org/jsource/History/Inquisition.html for more information.
Remember that in 15th century England the punishment for treason was to hang a man, cut him down while still alive, disembowel him, and then drag him in four pieces with horses or cut him in 4 pieces. “Hung, drawn, and quartered.” In France they boiled traitors. You do acknowledge that it was a brutal age compared to our own. That’s that.
Torquemada was appointed to reform the inquisition which was being used in unjust ways in the view of the Papacy. He actually reduced punishments.
Remember also that there is no question at all that the Jews in Spain worked with the Muslim conquerors and aided in the wars against Christians.
I don’t even think we can jokingly say that the Jews backed the wrong horse, since the Jewish population had 7 centuries of special privileges under the Muslim masters.