In an attempt to find a peaceful alternative for those in the Islamic world who advocate violence for political and religious goals, Christians in the West shouldn’t distort the history of Christianity, or stand idly by while others do so. Letting this version of events shape perceptions of Christian history invariably means a portrait of religion as a force of darkness, while science and technology will always be beacons of sanity and light.

The narrative portraying religious conviction as antithetical to reasoned comity among people and nations is easy enough to fall into. At the national prayer breakfast last week, for instance, President Obama compared the excesses of the Crusades and the Inquisition to the terrorism of today’s radical Islam. The president went on to condemn (rightly) those who advance their religious convictions with violence.

But what he and many others miss is the conviction that Western core values come from a faith in which God enters into human history precisely to save the world from the erring reason that fails, among other things, to recognize that terrorism is an affront to God and humanity.

The all-too-common narrative goes like this: Centuries ago, Catholics and Protestants gladly burned heretics up and down Europe by the thousands until, thank God—or All Powerful Goodness, as Ben Franklin would put it—the rise of Enlightenment thinkers banished the barbarity that is somehow native to religious fervor. Only with the liberalizing mandates of Vatican II (1962-65), we’re told, did Catholicism—usually the main boogeyman in this version of history—come to grips with the idea of democracy and religious freedom, and finally extinguish the last embers of the Inquisition.

This narrative is false according to the historical record and to the origins and abiding ethos of Christianity, Catholic and Protestant. Historians call this the la leyenda negra—the “Black Legend”—because it blackens the name of Catholicism in particular and religion in general. According to this legend, the Inquisition is on a continuum with the Holocaust and the terrors of Stalinism. ...