If you want to read a judicious and scholarly work on the Crusades that is an able defense of the just war theory in response to Muslim conquest, Rodney Starks “God’s Battalions: The Case for the Crusades.” Stark is a scholar at Baylor University who is not afraid to go against group think. I have read the book a couple of times and find it thorough. He exhibits a Christian horror of war and is careful to identify overreach and unjustifiable bloodshed on the part of those who fought in the name of the Christ. I recommend Stark’s works in general.
The Crusades, the Inquisition and the Salem Witch Trials are essentially cliches in today’s flattening out of the achievements of the West and of the Church in particular. In a world of much cruelty and horror the aberrations of the church barely show on the radar screen of history. They are real blips and warnings to all Christians who default to war as a response to persecution and oppression. They are a continued warning to a Church that forgets Christ’s kingdom is not from the this world. But in context Christianity escapes in large measure the pointing finger of those who in a multi-culturalists manner cannot allow Christianity its true accomplishments.
The recent uptake in pacifism among Evangelicals often rather ignorantly relies on these episodes to proof their points. See Brian Zahnd’s A Farewell to Mars: An Evangelical Pastor’s Journey Toward the Biblical Gospel of Peace. Zahnd does not credit Christianity with the natural instinct toward peace that resides within its DNA, not so much doctrinally, which it obviously has, but in actual history.