There was atrocities committed by both sides. War is war and it is far from humane. I'm not in defense of Christianity or saying the Christians were on the right side of this war, more to point out our history is one of religious war. It doesn't matter what the scripture say. What matters is that religion has provided man with the motivation to expand their control of others, in the "name of God".
I'm also not saying this is the Christianity or Islam of today, however I am saying it is a good thing it is not.
I'd disagree with that assessment. Mankind, as a whole, is prone to sin. In the hands of sinful men, religion becomes one more thing that they can abuse and corrupt for their own ends. Whether religious or non-religious, it should come as a surprise to no one that there are those who would use religion for personal gain and power.
That, however, does not mean that that is the purpose, intent, or value of religion. A scalpel's purpose is for surgery, to save and improve people's lives who are suffering from injury or disease. In the right hands, a doctor will use it as intended and help people. In the wrong hands, you get a bunch of dead bodies. The latter case does not invalidate or lessen the purpose, intent, or value of a scalpel in the right hands.
Now, different religions have different philosophies, intents, goals, etc. I won't say that all religion is fundamentally good - as I think there are religions, or at least sects within the various religions, which are fundamentally dangerous. That said, religions like Christianity exist to help people, to do what is right and good, and to teach others to do what is right and good. Indeed, the scriptures tell us that we were created for the purpose of doing good works. We are to love all - even our enemies who curse us. We are to give of ourselves to help those in need. We are taught that mercy is greater than justice. etc.
When evaluating whether various deeds are truly representative and inline with the intent of the religion under which people claim to act, we must compare those actions against what the religion actually teaches. If they murder in the name of God - does God actually call for them to murder, or does he tell them that it is a sin? When people defend racism under the name of God - what do the scriptures actually say? There is no Jew nor Gentile, Female nor Male, all are equal in Christ, Christ died for all, love one another, etc.