Too many people erroneously associate atheism with pacifism. Certainly, many pacifists, leftists and 'all people are brothers' types happen to also be atheist. Communism is partially to blame for that, but in part it's just due to the fact that atheism does not have any defined authority or creed so everyone can build an ideology they like.
In in itself, atheism or science for that matter, is not intrinsically pacifist, tolerant or accepting. If anything, science and history is more of the opposite of tolerance and acceptance. Take Evolution Theory for example, you do not need to connect too many dots to turn survival of the fittest into Social Darwinism, people like Herbert Spenser did just that. Social Darwinism is too extreme and effectively useless, but it's an example. One can use science and atheism to justify extreme intolerance and cruelty too, just like with religion. If that is the case, then wars too can be justified with science.
Since times of Roman Emperor Constantine, military and church shared an uneasy alliance of sorts. Reason for that was the fact that military needed priests and their sway over hearts of men to persuade these men to fight, kill and risk their lives in wars. This alliance was not easy, church's sway over people's hearts allowed priests to effectively control many aspects of live, especially during Middle Ages. Many kings and emperors were frustrated by this overreach by pesky priests who grew so powerful, they begun dictate their rules even to kings. Yet kicking off churches' yoke was much harder than it seemed. Church fought back with excommunications and inquisitions and good many kings found their men turning against them if church denounced them.
Yet until recently there was nothing kings could do, superstitions commoners trusted conmen in robes and their fictitious reasons to support or oppose various things. Despite that, even when atheism became mainstream and more and more people are now irreligious, military somehow kept clinging to religion. Reason for that is the fact that no matter how difficult conmen in robes are sometimes, they still rally men to war whenever they and military are in agreement.
However, is power of conmen in robes this unescapable? Is it really not possible to justify a war and rally people for it, using purely rational and scientific arguments? Turns out not. To see an example of how it could be done, one should study Nazi ideology.
Nowadays it's common to demonise Nazis and reduce their ideology to a banal emotional and irrational racial hatred. Something like that is useful as war time propaganda but reality is Nazi ideology is the fact that is based on very rational and common-sense self-interest arguments.
As much as historians like to point out that Nazi accusations against Jews are untrue, the arguments themselves were not based on hatred but on common sense bread and butter issues. A common German, rather impoverished due to economic problems in interwar times, responded well to Nazi arguments that Jews betrayed and robbed them. Jews were one socio-economic group that at least seemed well off during the times when everyone else was struggling. Regardless of whether it was true or not, first people grew to believe Jews were the problem, only then came Holocaust.
To mobilize Germans against external enemies, Nazis used all the same economic arguments. Poland and France robbed Germany of its wealth and it's only fair to march there with arms in hand to take back what is ours to begin with. Once again regardless of whether it was true or not, people believed in it and all rallied to the flag. The effect certainly exceeded all expectations, Germany did lose in the end, but it never had moral or loyalty issues. People fought to the end.
Economic arguments were not the only ones. Nazis also picked at their enemies' appearance and cultural traits. Nazis claimed that cultures or their enemies, both Jewish and Slavic were inferior to German one, thus is only fair to treat these people of inferior cultures as inferior human beings. Different examples of unlikable cultural traits were used to justify this point of view. Meanwhile eugenics dealt with outward appearance, judging people based on shape of their noses, forehead and the like.
I would argue that modern hatred of Nazis and demonisation of everything Nazi comes not from their crimes but from the simple fact that Nazis made church and its priests redundant. Anschluss of Austria and many further events showed just how swiftly power over people slipped through priests' hands as public ignored the conmen in robes and rallied to Hitler's banner. Thus, after the war, church did all in their power to reduce Nazism to mere racial hatred. They reasonably fear that if studied properly, Nazi ideas will allow government and militaries to wage wars without church approval and that will eliminate the remaining moral authority they still wield over society.
The Nazi example clearly shows that people are more than willing to listen to rational and scientific arguments for war and willing to support wars too, if they serve their self-interest. One should simply explain to them how they personally will benefit from that.
Thus, governments and militaries no longer need God or priests to rally people for war, science, logic and reason can do this too. If fact by now religion is probably more of an obstacle than a boon. Religious arguments sound so silly that a good number of people will simply ignore the argument if the church or priest endorses it. Thus, government and military have no choice by to learn to operate in new reality and base their arguments for war on rational and scientific arguments.
However, there is also a newfound freedom in doing things new way, sure not every war can be justified easily, and certain skill is needed to connect all the dots to sway public opinion. One has to be more specific and precise in pinpointing the problem or public will not buy it. However, there is clear advantage as priests no longer have any say and old system too had their own constraints, like justifying wars against fellow Christians. Many wars we will likely see will be against Sub-Saharan Africans who are mostly Christians.

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