Interestingly enough, I did a paper on this very question in my bachelor (comparative religion). My case study was Sri Lanka, but I'll give examples from other nations here as well, for a more 'universal' approach.
There are three means of reconciliation of violence and Buddhism I will distinguish here. Incidentally, these are not unique to Buddhists. Other religions handle their formal rejection of violence in a similar manner.
First, Buddhism, like other religions, is linked to cultural and national identity. Buddhists would fight in protection of their nationstate and what they perceive as the "keepers of the tradition". They apply a larger-than-life mentality to the warfare. That is to say, the importance of continuing the tradition outweighs the views on morality they hold. (Daniel Kent (2010), 'Onward Buddhist Soldiers, Preaching to the Sri Lankan Army' in: Buddhist Warfare)
Soldiers don’t shoot the enemy out of personal anger. If they shoot they do so for the common good. This war is on behalf of the country, people, religion, region, and motherland. It would be negative karma to shoot one’s neighbor over a land conflict, but the intention here is a good one.
Second, there are attempts to de-humanize the opponents. This is very similar to Christian and Islamic justification of violence. Opponents are represented as possessed by demons, thereby transforming the violence from a mortal to a sanctified action. (in: Michael Jerryson (2010), 'Militarizing Buddhism, Violence in Souther Thailand' in: Buddhist Warfare)
[B]ecause whoever destroys the nation, the religion, or the monarchy, such bestial types [man] are not complete persons. Thus we must intend not to kill people but to kill the Devi [Māra]; this is the duty of all Thai.
Third, karmic sacrifice. This is a classic case of multiple interpretations of (somewhat) ambiguous theology. Some individuals are considered such sinful beings, that they will only commit more crimes the longer they live. Killing these individuals can be considered a heroic act, because the killer will sacrifice his own karma in order to prevent the victim from committing more crimes and going to hell. (in: Derek Maher (2008), The Rhetoric of War in Tibet)
[K]illings [can be] undertaken in order to preserve sinful opponents of Buddhism from committing worse crimes that could be expected to earn them more severe karmic retribution than if they had not been killed.
Lastly, on a more personal note (hope that's allowed) there are some understandable misconceptions about Buddhism. (these same misconceptions incited my initial question for the aforementioned paper). Buddhism has many forms. And the majority of those forms has aspects similar to other religions. Please don't believe that "Buddhism is more a philosophy than a religion". Many forms of buddhism have gods, demons, heaven, hell, prayer for help, and rituals with magic properties. Therefore, evil and violence toward perceived evil is not at all uncommon among buddhists. If someone tells you that that is not real Buddhism, that would be a theological belief, not a statement supported by scholars.
A really interesting case study on this is japan during WWII and Zen Buddhism.
Two important works on this topic are "Zen at War" and "Zen War Stories " by Brian Daizen Victoria. These books examine how Zen Masters justified and contributed to pro war propaganda.
Here are some quotes from Zen masters during WWII:
"[If ordered to] march: tramp, tramp, or shoot: bang, bang. This is the manifestation of the highest Wisdom [of Enlightenment]. The unity of Zen and war of which I speak extends to the farthest reaches of the holy war [now under way]." - Harada Daiun Sogaku
"Showing the utmost loyalty to the emperor is identical with engaging in the religious practice of Mahayana Buddhism. This is because Mahayana Buddhism is identical with the law of the sovereign." -- Seki Seisetsu
. "I wished to inspire our valiant soldiers with the ennobling thoughts of the Buddha, so as to enable them to die on the battlefield with confidence that the task in which they are engaged is great and noble. I wish to convince them.... that this war is not a mere slaughter of their fellow-beings, but that they are combating an evil." -- Shaku Soen
"In the present hostilities, into which Japan has entered with great reluctance, she pursues no egotistic purpose, but seeks the subjugation of evils hostile to civilization, peace and enlightenment." -- Shaku Soen
So what we are seeing are men who are just as susceptible to nationalism as anyone else who are able to justify aggression using twists of Buddhist logic. Its the nature of belief structures that they can always be twisted to support a world view.
Also, understand that not every "Buddhist" "takes the full precepts". The full precepts would only be taken by Buddhist monks and nuns who "renounce the world". The average soldier would not have necessarily taken any preceipts personally. Even if a soldier has received something like the Soto Bodhisattva precepts which includes instructions not to kill, these types of things can be twisted subjectively.
For example:
""It is just to punish those who disturb the public order. Whether one kills or does not kill, the precept forbidding killing [is preserved]. It is the precept forbidding killing that wields the sword. It is the precept that throws the bomb." -- Sawaki Kodo
One of the more interesting one cases of Buddhism and war is Japan.
Historically Buddhism in Japan has being subordinated to the state and began as a religion of the upper classes. between the 10th and 17th centuries Buddhism temples and monasteries were incredibly powerful and military orders of warrior monks (not unlike Christian military orders like the knight templar), known as the Sohei. Those orders fought both to defend their own temples and in attacking rival sects. They eventually grew so powerful that they were viewed as major threats by would be unifiers of Japan during the Sengoku era. Nobunga, Hideyoshi and Tokugawa defeated them and banned them under in Tokugawa Japan.
That did not end the relationship between the state and Buddhism became a defacto state religion in the Shogunate, where families had to associated themselves with a nearby Buddhist temples. Buddhism in Japan was therefore subordinated to the state.
Zen Buddhism had always being favored by Japan's warrior classes, the sect advocated indifference between life and death, and stressed the importance of discipline and that of an austere life style. During the 20th century Zen Buddhism became actively involved in promoting war, especially during WWII.
They justified it by:
Religion must support the state at all costs, because should the state ever collapse then the chaos it produces would in turn produce far greater violence than otherwise
Killing could be justified if the people killed are "evil", and that failure to kill evil men actually constituted a breach of Buddhist beliefs. It is not compassionate, for instance, to let an evil man live so that he can harm others later on.
The war being fought in East Asia was a "just war" based on eliminating western colonialism in Asia and the establishment of a greater Asian co-prosperity sphere, and hence on the long run, eliminate war.
The emperor is an ultimate enlightened being and thus deserves special moral authority.
There were of course, dissidents to militaristic interpretation of Buddhism, but as religion was subordinated to the state, views favoring the needs of the state tended to be much more popular.
Sources: Critical Buddhism: Engaging with Modern Japanese Buddhist Thought By Mr James Mark Shields
Zen at War by Brian Victoria
This is fascinating and a question I'd wondered about myself -- particularly as I'd mostly fallen for the sanitized version of Buddhism popular in the West.
On the one hand, these explanations indicate that Buddhism is largely like other religions in formally eschewing violence, but finding convenient exceptions when necessary.
Given the great commonality among religions in this regard, I wonder if a further question might be whether there are any differences between Buddhist-majority nations and other-religious-majority nations on this subject -- and differences that might plausibly be attributable to Buddhism itself (and not merely attributable to common geographical or historical circumstances).
For example, is there anything in the ongoing rapid reconciliation between Vietnam and the United States (particularly as compared to the ongoing wars in the Middle East or Nothern Ireland, etc.) that is attributable to Vietnam's majority Buddhism? Or is that simply a red herring that merely clouds the decisive role of historical circumstance?
Also, I recall that in China, some of the early Qing emperors, I think, were devout Vajrayana Buddhists, but also were quite militaristic and violent -- responsible for just as many atrocities as other emperors. I would be grateful if anyone knows of this and could elaborate? Thanks!
Are we allowed to discuss the Burmese's treatment of the Rohingya here? Or is that too recent, even though it goes back to 1948?
Anyone know of good books on king ashoka rule over india, that was a buddhist kingdom