This question was inspired by an argument with a man who believes that Christianity is essentially pacifist and peaceful, while Islam is essentially violent, or at least more condoning of violence than is Christianity. When I pointed out that Christianity has not been interpreted in an ultra-pacifist manner by most people in history, and that it is just as capable of being interpreted in a violent manner as Islam, he responded by saying that medieval and early modern religious violence was the result of the corruption of the Catholic Church, which misled believers. Now leaving aside the absurdity of that, what strikes me is that this man (and presumably many others like him) was so convinced of Christianity's fundamentally pacifist nature that he was willing to declare that millions of believers across more than a dozen centuries were misinterpreting the faith.
There's obviously a major disconnect between the way many people think of Christianity today and the way that the religion has manifested itself in the past. Why the change? How did medieval and early modern Christians justify violence and why are those justifications no longer accepted by modern-day Christians? How do modern-day Christians justify pacifism, and why would those arguments be rejected by medievals and early moderns? Of course, pacifists have existed historically as well, and there are plenty of people alive today who do use Christianity to justify violence, but I am interested here in mainstream interpretations.
I'd also like to clarify that I'm not asking about which is the correct interpretation of Christianity, since I believe no such thing exists, religion is just what people make of it.
I can speak a bit about the crusades, Catholicism, and religiously ordained violence The Crusades were one of the first examples of religiously ordained violence on the part of Christianity. Before this, you could have religiously motivated warfare - Bede in the 700s discusses righteous Christian kings who killed pagans, but it is the kings themselves who are religious, not the killing or the warfare itself.
This changes in 1095 at the Council of Clermont when Pope Urban II calls for a crusade to aid the Byzantine Empire and retake the Holy Land. The Gesta Francorum, Fulcher of Chartres, and Guibert de Nogent's accounts all describe the Pope offering absolution or remission of sins for those who would take the Cross. The idea of pilgrimage, or a journey to the Holy Land to prove ones worth, had existed before, but this was one of the first instances of religiously ordained violence for the remission of sins. However, this Papally ordained war was specific in scope: just to Jerusalem, just for the Holy Land.
This would change. The next several centuries became a widening of targets for religiously ordained violence. When crusades began, they were often accompanied by pogroms on the local Jewish communities such as in Mainz in 1095; though church authorities often attempted to stop this, these killings normalized the massacre of Jews for religious reasons. The Second Crusade to save Edessa, and the Reconquista for Iberia showed that Jerusalem was no longer central to religiously ordained violence, it could be directed at any enemy of Christendom. The Fourth Crusade in 1204 that sacked Constantinople, and the intensely political Albigensian crusade in southern France indicated that even Christians could be the target of religiously ordained Christian violence. Religiously ordained violence was used to justify the crusades of the Teutonic knights in Lithuania, showing that pagans who had previously been the target of conversion could now also be the targets of Christian violence.
The crusading fervor died in the 1500s and 1600s as the Reformation tore Christian Europe in two and the New World offered more promising opportunities abroad. The Enlightenment too was not friendly to religiously ordained violence and the crusades: David Hume wrote of the crusades in 1776 that "Europe was at this time sunk into profound ignorance and superstition: the ecclesiastics had acquired the greatest ascendant over the human mind: the people, who being little restrained by honor, and less by law, abandoned themselves to the worst crimes and disorders, knew of no other expiation than the observances imposed on them by their spiritual pastors; and it was easy to represent the holy war as an equivalent for all penances...". Edward Daniel Clarke and Edward Gibbon were similarly unfriendly to the crusades in their works. In an intellectual world that was increasingly interested in humanism and the scientific method, the idea of religiously ordained violence had fallen far out of favor in Europe.
Chronologically, this is about where my field of knowledge ends. Romantic authors in the 1800s revived the idea of the crusades and religious violence as positive, but modern Christian theories on violence are many and multifaceted. This answer is also very Latin-centric; Orthodox and Eastern churches have very different theories on violence. Despite these limitations, I hope my answer helps explains how the crusades developed and expanded the definition and targets of religiously motivated violence.
Sources
Anonymous. "Gesta Francourum et aliorum Hierosolimitanorum: The Deeds of the Franks and Other Pilgrims to Jerusalem" Translated by Rosalind Hill. In Chronicles of the First Crusade, edited by Christopher Tyerman. London: Penguin, 2011.
David Hume, The History of England, from the Invasion of Caesar to the Abdication of James the Second, 1688, 1776
"The Chronicle of Fulcher of Chartres, Book I (1095–1100)." In The First Crusade: "The Chronicle of Fulcher of Chartres" and Other Source Materials, edited by Peters Edward, 47-101. University of Pennsylvania Press, 1998. http://www.jstor.org/stable/j.ctt3fhh0t.7.
Geoffrey de Villehardouin. Memoirs or On the Conquest of Constantinople. Translated by Frank T. Marzials, (London: J.M. Dent, 1908).
Pope Innocent III, Ep 136, Patrologia Latina 215, 669-702, translated by James Brundage, The Crusades: A Documentary History, (Milwaukee, WI: Marquette University Press, 1962), 208-09.
Robert of Clari. The Conquest of Constantinople. Translated by Edgar Holmes. McNeal. New York: Columbia University press, 2005.
Asbridge, Thomas S. The first crusade: a new history. New York: Oxford University Press, 2005.
Frankopan, Peter. The First Crusade: the call from the East. Cambridge, MA: Belknap Press of Harvard University Press, 2016.
Harris, Jonathan. Byzantium and the Crusades. London: Bloomsbury Academic, 2014.
Lambert, Malcom. God's Armies: crusade and jihad - origins, history, aftermath. S.l.: Pegasus Books, 2017.
Nicol, Donald M. Byzantium: its ecclesiastical history and relations with the western world - collected studies. London: Variorum Reprints, 1972.
Phillips, Jonathan. The Fourth Crusade and the Sack of Constantinople. New York: Viking, 2004.
Queller, Donald E., and Thomas F. Madden. The Fourth Crusade: the conquest of Constantinople, 1201-1204. Philadelphia, PA: University of Pennsylvania Press, 2000.
Riley Smith, Jonathan.The Oxford Illustrated History of the Crusades, edited by Jonathan Riley-Smith. Oxford University Press, 1995.
Early Christian theologists spent a lot time and effort debating the extent to which violence could be justified. Augustine of Hippo was a particularly influential in developing the theories of Christian jus bellum or Just War, coining the term itself in The City of God. The theory holds that, while violence is always bad, it can be justified if the results of no violence are worse. The answer, therefore, to "war, huh, what is it good for?" is self defence, or the defence of the wider peace.
In Contra Faustum Manichaeum, Augustine says that: They who have waged war in obedience to the divine command, or in conformity with His laws, have represented in their persons the public justice or the wisdom of government, and in this capacity have put to death wicked men; such persons have by no means violated the commandment, "Thou shalt not kill."
Specifically, God in Romans 13:4 gave kingdoms a sword, and a legitimate authority to mandate violence in defence of themselves and the law, which at this point is also synonymous with the Church. Therefore violence can be excused if it is legislated by the state or church to punish sin or transgression.
How this is applied varies between nations. Alfred the Great's defence of England against the Vikings, for example, is praised in the Anglo-Saxon Chronicle for defeating the invading Pagans. Even during the reign of Æthelred the Unready, the ASC takes pains to illustrate how Cnut - a Christian - attacks churches and monasteries, and so violence against him is extra-justified.
In 1066, the Norman Conquest of England is justified by William of Normandy and Bishop Odo as punishment for Harold Godwinson's transgressions, specifically swearing an oath on holy relics to give William the throne and then reneging. This can be further seen in the Bayeux Tapestry where Harold loses his eye - the biblical punishment for oathbreaking.
The most outward expression of Just War is the Crusades. Pope Urban II justifies the call to crusade as a war to defend the Holy Land and the Christians suffering under Muslim oppression. Whole books have been written on the actual reasons behind the crusades, but the justification is neatly framed as a just war necessary to protect both the history and future of Christendom.
In the twelfth century, the Anglo-Norman kingdom of England also uses Just War to justify their invasion of Ireland. According to Gerald of Wales, not only are the English invited by Deirmod to end a rebellion against him and restore peace, but they also are morally compelled to end a wide variety of sins carried out by the Irish, which are extensively detailed by Gerald's Topographia Hibernica.
The theories of Just War are later expanded by Thomas Aquinas in Summa Theologica where he establishes three main tenets:
1 - War must come from a legitimate authority.
2 - The purpose must be good, and not self-interest: The punishment of sins, the restoration of lost territory, goods, rights, or the defence of same.
3 - The end goal must be peace: the thwarting of an invasion, perhaps, or the prevention of attrocity.
These rules are used to justify an array of conflicts, largely because of the conflation of royal and religious authority in concepts of medieval kingship. The Albigensian Crusade, for example, is justified as the king has a duty as moral guardian, and to not address the Cathars' secession from France would not only undermine his political power, but would thus also endanger the souls of all of France. Similar logic is used by Franz von Waldeck for the brutal suppression of the Anabaptists at Münster in 1534-5. Whilst adult baptism may seem logical by today's standards, by the religious standards of the 16th century, the practice condemned the souls of any dead children to an eternity of purgatory instead of Heaven, and as such would be unconscionable.
Some additional sources:
Bartlett, The Making of Europe
Gillingham, The English in the Twelfth Century
Tyerson, God's War
MacCulloch, Reformation: Europe's House Divided