The Crusaders perpetrated a century of genocides that murdered a million people, equivalent as a proportion of the world’s population at the time to the Nazi holocaust.
One of the first things you must learn about history that the large numbers in medieval and ancient chronicles rarely correspond to the literal truth. "100,000 men" doesn't mean that the chronicler actually had access to an actual count: it just means that it was a very large army. And almost always, the large numbers are inflated.
Since there were nine numbered Crusades in just under 200 years, a million deaths would require over 100,000 murders per Crusade.
This is profoundly unlikely.
Even if we assume that half the dead were civilians, this requires the average Crusade to consist of an army of 40,000 strong fighting to the death and an opposing army of the same size suffering 25% dead.
But our best evidence is that the armies were much smaller and less willing to die.
And the Crusades stretched over seven generations, so the denominator is seven generations of lives, not one.
Also, although there were atrocities, I do not think the Crusades were as a whole genocidal in intent.
I can't shake the impression that Pinker doesn't like religion much, and is at best careless in his examination of evidence that supports his bias.