Humanity has been grappling with these questions throughout human history. And lest we get on our high horse and think this is unique to some other place, remember that during the Crusades and the Inquisition, people committed terrible deeds in the name of Christ. In our home country, slavery and Jim Crow all too often was justified in the name of Christ.
Quite often people, apparently including some western world leaders, display a stunning lack of knowledge or understanding of history by blindly dismissing the crusades and the inquisition as nothing but Christian fanaticism, comparable to the exploits of ISIS and Al Qaeda. It pays to read up on some background here.
Before the rise of Islam, North Africa and the middle east were largely Christian. The largest Christian communities of the area were in present day Egypt and Turkey. This represented a large percentage of the world's Christians, as Northern and Western Europe were comparatively sparsely populated at the time. These areas did not peacefully and voluntarily convert to Islam. During the lifetime of Mohammed, the Byzantine and Persian empires were engaged in a war against each other that lasted a century, and crippled both empires to the point that they were unable to resist the Arab invasions when they came. The Persian empire was completely absorbed, while the Byzantine empire lost Egypt and the Levant. The Gothic kingdom in Spain was completely destroyed by Muslim invaders, and only a fairly unlikely victory by Charles Martel at Tours kept the Frankish empire from falling too. Had that happened, all of Europe would likely have ended up under Islamic rule. Eventually the Umayyad broke up, and stopped expanding into Europe.
tl;dr In short, Christian leaders at the time of the Crusades had some reason to feel threatened by Islam.
Fast forward a few centuries. During the 11th century, the great schism happened: The Christian church had broken up into two competing halves: Catholic and Orthodox. Around the same time, the Turks invaded the Arab world, and conquered most of it. They converted to Islam, and started unifying Islam again. Once again, the Christian world saw itself confronted with an Islamic invasion. The Byzantine emperor asked the Pope for mercenaries to help defend against this invasion. The Pope saw an opportunity to reunite the Church, and asked for volunteers. Thousands of responded. Motives may have been a mixture of genuine piety and a wish to liberate the Christian brothers of Syria and Armenia on the one hand, and a quest for glory on the other hand, but to simply dismiss their motives as fanaticism or western Imperialism does them great injustice.
tl;dr The crusaders may have had good reasons and decent motivations.
As for the inquisition, you once again have to look at the background. The great schism I wrote about before was never resolved, and by the early 16th century, almost the entire Eastern Orthodox half of Christianity had been occupied by the Islamic Ottoman Empire, which extended as far as Central Europe and threatened Vienna. It was the major superpower of the time. During the early 16th century, a new great schism was starting to form: regions in Europe started to convert to Protestantism and breaking away from the church. The inquisition should not just be seen as a display of fanatical intolerance, but as an ultimately failed attempt to prevent Christianity from splitting in half once again right at the time of its greatest threat from Islam. The inquisition understandably got a very bad name in protestant countries, as a number of prominent protestant leaders were executed, but it wasn't a bloodbath on a massive scale. Roughly 10 times as many people are killed per year in traffic in the USA.
tl;dr The inquisition's motives were more complex than fanatical intolerance alone, and Obama's drone body count isn't all that impressive
Finally, as for slavery, it was abolished in Europe during the middle ages. The church forbade enslaving fellow Christians, and Europe ran out of heathens. The institute of slavery was kept alive on the other side of the Mediterranean, where the various Islamic states kept Europeans and Africans as slaves. This turned out to come in handy when Europeans started to colonize the new world, and started looking for manpower to buy...