First , we need to examine the premise of your question. I would argue that Christianity has caused almost no wars, and killed very few people. Actually, this is relatively true of religions in general. Wars are caused by the greed, for either wealth or power, of individuals and peoples. Sometimes those individuals and peoples try to wrap their greed in the cloak of a religion to disguise it or inspire their warriors, but that is not the root cause. But lets examine a few examples, for this is not always clear.
The Crusades would be the first example most people would come up with. This is the closest I can come to finding a truly “holy war” since the dawn of Christianity. I do think many of the Christian participants had religious reasons for taking part because many lost their personal fortunes and their lives in these expeditions. On the other hand, when you read some of the letters written by Crusaders before they left, not all had pure motives at all. The Crusades did likely rescue western civilization and Christianity as we now know it from Muslim “crusaders”, so it could have been used by God in that respect. But many crimes against humanity were committed by the Crusaders. That is humanity, not God, and I will touch on that later.
Every other conflict I can think of, was clearly not a Christian war at all. Even the 30 years war between the Pope and the Protestants was clearly a land and power grab with players on both sides switching allegiances to suit their own greed. The modern conflicts in Ireland between Catholics and Protestants are not about transubstantiation or whether the books of Maccabees should be in the Bible. They are about control of the Irish government or the local business district. Even the conflict between Israel and Hamas is really about control of a strip of land that both groups controlled in the past and want to control again.
But there have been witch hunts and inquisitions and awful crimes by Crusaders. How could this happen if God is holy, good and all-powerful?
Again, we are back to the free will of man. God absolutely wants, in the finality of eternity, to end up with a family of people in heaven who freely choose to follow him. Therefore, even in his church, human beings can choose to do terrible evils. God is willing to have his name abused and his character appear to be offended, so that no man can say they did not have a choice. We cannot blame God for the choices of man. That is not reasonable in any sense. Anything that includes man, will be imperfect and at sometimes evil so that every man is always offered a clear choice. You would do the same if you were God, for there is no other realistic way to accomplish a true “heaven”.
People form groups to gain power. For proof of this, look no further than the cliques in any local school, elementary through graduate schools. Sometimes people use established groups to gain their own power (nations, tribes, skin color and religion). That doesn’t mean it is what God wants. Some would say that God is awful for allowing such evil and suffering, even if that is the only way to achieve a true heaven, but that is only true if you view this life on earth as the only life there is. If however we are eternal beings, then God has all eternity to reward and punish so the amount of suffering any of us endure here on earth is almost irrelevent.
Lastly, lets compare the crimes of Christianity, to the crimes of atheism. The combined death toll for the inquisitions, the witch hunts, and the non-combatant deaths of the Crusades is surely less than 200,000. That is a lot, especially when you consider the population of the world at that time. But consider atheism in just the last 100 years. Adolf Hitler (fascism was based on the works of Nietzsche), Joseph Stalin and Mao Zedong were clearly all not trying to live their lives as disciples of Jesus and likely atheist. Their minimum combined death toll is 60 million, probably much higher. Atheist writers want to make the loosest connections possible between Christianity and wars, and then claim atheism is not related to the crimes of these three men. You cannot have it both ways. I don’t like the idea of counting crimes because I want to keep these answers philosophical in nature, but to ignore this would be to fiddle while Rome burns.[cref logically-christian Logically Christian Home Page]