In the context of its times the Inquisition wasn't all that bad a bunch - for one they tended to require some decent proof of guilt, which wasn't exactly a consistent line among temporal courts... They also tended to be fairly lenient all things considered - most of the people investigated (and not found guilty) were eventually sentenced to some suitable methods of penance if they admitted the error of their ways and repented. Torture was normally only resorted to if less drastic investigative measures were stymied (and this might take up to a year...), and even when used tended to be frankly bland and unimaginative. Particularly in comparision to the disquieting inventiveness shown by the temporal authorities, but then again they normally used torture as a form of public corporal punishement (ie. cautionary example; the common folk tended to consider it a good show...) whereas the Inquisitors were actually trying to interrogate someone instead.
Anyway, most of the time they concentrated on chasing after heretics, apostates and the like, which isn't exactly surprising if you remember that the Inquisitors' main job was in practice the upholding of Catholic institutions and faith. The pre-Reformation Church was actually a fairly laid-back outfit - so long as you paid your dues and didn't try to challenge them in some fashion, they didn't actually care too much of what you did or believed in.
Start trying to tear down their cozy little setup, though, and the worst-case result would be Cathar Wars and Albiguensian Crusades...
Anyway, whatever debatable good the Reformation did it most certainly ushered in some one and half hundred years of near-universal religious fanaticism, persecution, atrocity and general unpleasantness that didn't really quiet down before the mind-bogglingly destructive Thirty Years' War which was in many ways extreme enough to make all but the fringe loons take a step back and seriously reconsider.
As a side note, witch-hunting tended to be more of a King Mob and local authority pursuit. They tended to be the ones to pay the professional with hunters too, who as they were paid by the number of witches found andto boot tended to get the choicest pickings of the late sinners' worldly possessions had a certain incentive to be excessively competent... Most of the time if an Inquisitor or just plain higher temporal authorities got involved - ie. someone actually studied the charges, suspect and evidence with any detail - the suspected witch ended up walking away a free man or woman due to massively insufficient proof. Heck, the first serious investigation into the phenomenom of witches et all was by a Spanish Inquisitor who went around for quite a while doing research and ended up with the conclusion it was so much superstition and hysteria... However, the Inquisition was anything bu a monolithic organisation and the views of its local and individual representatives naturally varied widely; there was certainly no shortage of fanatical arsonists in the ranks either.
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