Hmm, a bit of googling on the author of your second link gives the impression, that, while being a respected academic, he also seems to have made a bit of a career as an apologist for the various failings of the Christian churches over the millenia. I am not at all an expert on these matters, and of course haven't done extensive research on the guy, so I may be wrong, but personally from what I've seen in the last few minutes I'd take his words with a grain of salt.
Anyway, neither of the two links you gave deny that the Inquisition did actively seek out and persecute people who did nothing more wrong than hold personal beliefs not in accordance with that of the church. How right or wrong the Inquisition was in relation to what else was going on in the world at the time is of little interest IMO, that argument can be used to justify almost any atrocity ever. So I'm not sure its so very wise of you to say you'd be proud of being associated with them (if that is what you were saying), given that you don't otherwise come across as a guy who's proud to be persecuting people :-).
Oh god, this is so OT ;-). In an effort to justify my posting let me say that I heartily approve of the new XP system, and also of the phoenix-like transformation of the Grand Inquisitor to a Sage.
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