Neither the Crusades nor the Inquisition were 'misguided Christians' who didn't know what they were doing. The Crusdaes were simply a land grab using the "Holy Lands" as an excuse. IIRC, more mid-east Christians were killed than any other group. The Inquisition was a political power play. I believe it was reluctantly given support by the church early on when they didn't know how far it would go. Like the Anglican split from the Catholic Church, it was a strange mixture of politics and religion by people far more focused on the politics while using the religion as a facade

Problem with Christianity is that anyone can claim to be a Christian and then their actions reflect on all Christians and Christ. But as Jesus said "You will know them by their fruit"