The problem comes sometimes from taking things that have some truth and embellishing it.
There were many heretics killed to preserve the faith. It is sad but true. The Church in the past took the role of protection of souls too far, even to death. That is the past and things were different then, what is considered barbaric now was common then. I would point out that all religions have killed those not of their beliefs.
The protestants killed thousands of Catholics after the reformation, the Puritans killed people suspected of witchcraft and so on and so on.
That doesn’t make it right then or now, but that was the times and culture then.
The Inquisition was mainly a way to preserve power whereby King Ferdinand and Queen Isabella used the church eliminate those they perceived a threat. It is unfortunate that they were able to find clergy willing to cooperate.
One of the causes of the reformation was the buying and selling of indulgences by the pope and bishops who were hungry for money to subsidize their lifestyles as well as build great churches for their legacies. These were shameful people, but the church past and present is made up of sinners. Jesus said that those were who He came to save.
As for the crusades, that the Church started Islam to take back Jerusalem just makes no sense. Jews and Christians lived in the Holy Lands for the most part peacefully. There was no need to take back Jerusalem until the Muslims conquered it.
What is important is to take time to investigate some of these things. Acknowledge that the church has things in its past and present that are shameful. But, remind your friend that the church, while guided by the Holy Spirit in faith and morals, is made up of sinners and with the grace of Jesus and the wisdom of the Holy Spirit, she is led ever deeper into truth.