First, as Christians we must acknowledge that violence in the name of Christ did indeed occur through the Crusades and other movements, and that it was real and very wrong. Using Scripture to force conversion (misusing the statement from Luke 14:23 to "compel them to come in") completely violates the free will God has given every man to choose or reject his Maker.
Second, it should be pointed out that the reason such an argument is effective against Christianity is because of the contradictory nature of the actions committed by the misguided individuals who led such campaigns. In other words, their actions betray the peaceful and respectful nature of Christianity and do not represent the teachings of Christ.
Third, it should be noted that the violence and death spread by naturalism and atheism has far exceeded that of events like the Crusades. Further (and perhaps more troubling) - while the violence initiated by Christianity was in direct violation of its teachings, the death and violence spread by atheism and naturalism are in perfect harmony with their philosophical teachings (e.g. Sartre, Nietzsche, etc.)
R. J. Rummel, in his book “Death by Government” records the following deaths by atheistic, anti-religion governments:
- Joseph Stalin 42,672,000
- Mao Zedong 37,828,000
- Adolf Hitler 20,946,000
- Chiang Kai-shek 10,214,000
- Vladimir Lenin 4,017,000
- Hideki Tojo 3,990,000
- Pol Pot 2,397,000
Rummel says, “Almost 170 million men, women and children have been shot, beaten, tortured, knifed, burned, starved, frozen, crushed or worked to death; buried alive, drowned, hung, bombed or killed in any other of a myriad of ways governments have inflicted death on unarmed, helpless citizens and foreigners.”
So while we as Christians should not shirk off the despicable acts that have wrongly been committed in the name of Jesus, eliminating the true religion of Christ is no cure for the world's ills. Wrong actions will always spring from wrong beliefs like atheism. Even some anti-God philosophers have observed the horrible things that can happen when people believe lies and act upon them:
"Those who can make you believe absurdities can make you commit atrocities."