Same with every one of those acts.

Crusades: Fear of the military power and expansion of the Muslim Caliphate. Putting it this way it sounds like a legitimate concern. The Muslims were in fact really good at fighting and conquering.

Persecution of Heretics: The Church was the focal point of people's trust. Renegade clergy could easily use their position of authority and respect to organize people into violent movements. Fra Dolcino, Martin Luther, and others.

Spanish Inquisition: The Church (with huge support from secular government; in fact, the Inquisition began as the Spanish Monarch's idea) felt that society was getting destabilized by the presence of Jews, Protestants, and non-Christians. Homogenous societies are in fact more stable than multi-cultured ones.

Confederates in the Civil War: They saw the North's opposition to slave trade as rivalistic ploy to destroy the Southern economy. They believed that without slavery their economy would be poorer (and this was true). They were fighting for their economy, livelihoods, and pride, not for Protestantism.

9/11: The hijackers and terrorists have specific political aims. Islam does not imply terrorism.

reminder It isn't that they acted justly, not at all, but in each instance the actions were done for the sake of some or other practical concern.