Induvidual instances of atrocities committed by an army does necessarily negate the justice if the cause being fought. The cause of the crusades, especially the First Crusade, was extremely just. Islam waged a 1000 year war against Christendom. After winning, by force of arms, the Levant and Northern Africa, they turned their attention to Europe, the heart of Christendom. Invading through the Iberian Peninsula, Sicily/Italy, and Asia Minor. These attacks were relentless. 400 years into it, the Crusades were a just attempt to take the offensive.
Despite their eventual defeat, the Crusades were likely successful, in the grand scheme of things in preserving Christensen.