Well the Inquisition was authorized by the Church, so you have to be very careful about how you argue the case to your friend. I don’t have a particular source to point you toward, but I would say that the best way to point yourself in the right direction is to focus on the bickering and disputes between popes and kings, as other posters have mentioned.
Most of the worst abuses committed by the Church in countries like England, France, and Spain, were due to the monarchy taking over control of church matters from the pope in Rome. In those days, we must remember, the pope often had shockingly little control over the selection of bishops. Nearly all of medieval history was little more than a continual struggle between church and state. If a particular strong king wanted to select his favorite cronies as bishops and administrators of his own national inquisitions, then there was often little that the church in Rome would do to oppose that.
None of this is to suggest that the Vatican was blameless for what happened. Far from it. Some popes resisted kings valiantly, but some popes were fawning accomplices… which makes sense because some popes were themselves cronies of kings who conspired to get them elected by corruption of the electing cardinals.
So tread carefully in all arguments you make about subjects like these, because there are blurred lines and gray zones of truth everywhere you look. The Spanish Inquisition was mostly a runaway abuse of royal power (ironically by a king who had no personal animus to Jews at all, but who simply used the persecution of Jews as a cynical tool to retain more secular power) that was opposed by the Church in Rome, but it was also something for which the Vatican showed cowardice by not opposing strenuously enough.
As a general rule, that can be said of almost all the medieval church abuses that took place under secular rulers. Sometimes the Church was brave in opposing them, and sometimes the Church was craven in giving sanction to them and making cynical power-sharing deals with royals when it shouldn’t have.
The key to remaining in the Church is to point toward the infallibility of dogma rather than the purity of historical actions. Which is not to say that actions should not inform faithfulness to the Church, since “by their fruits you shall know them”, but that’s a wide-spanning general admonition when viewing centuries of progress of Western civilization under Catholic leadership. It doesn’t necessarily mean that the leadership of the Church will always play the role of the good guys.
expects the Spanish Inquisition!" Monty Python’s Flying Circus.