Atheist
Don't the Crusades and Inquisition disqualify the Church's moral authority?
The Church, made up of sinful members, has committed and confessed real historical wrongs in these episodes, but the Gospel itself, not the failures of some of its members, remains the standard by which even those wrongs are judged and repented of.
Catholic teaching
The Church distinguishes between her divine mission and the sins of her members throughout history; Pope St. John Paul II's 2000 'Day of Pardon' publicly asked forgiveness for sins committed in the name of the faith, including violence done in the Crusades and the Inquisition, without denying that both had complex causes alongside religious ones.
Biblical foundation
Christ explicitly rebukes the use of the sword for his kingdom, 'those who take the sword will perish by the sword' (Matt 26:52), and teaches love of enemies (Matt 5:44), the very standard by which the Church herself judges these historical failures as genuine betrayals of the Gospel.
Scripture references
Historical evidence
Modern historical scholarship shows the Crusades began largely as a defensive response to centuries of territorial conquest and appeals from besieged Eastern Christians, and that Inquisition tribunals, while capable of real cruelty, generally followed far more due process and had far lower execution rates than contemporary secular courts of the era.
The Church Fathers
“We forgive and we ask forgiveness... for the sins committed in the service of truth by resorting to methods of intolerance and even violence.”