There's a Quaker joke that sort of addresses this. A Quaker farmer hears someone moving around downstairs. He grabs his shotgun and starts down the stairs, surprising a burglar. He tells the burglar "excuse me friend, but thou stands right where I aim to be shooting." The moral being, I guess, that there's nothing about pacifism that precludes self defense, but avoiding violence is still paramount.
In the case of World War II, the threat the Axis countries posed to the rest of the world was imminent, so if there ever was a just war, that was it. But some things about it that make it less than an unambigously good thing: First off, the Shoah was not stopped. Six million jews (and gypsies and homosexuals etc) murdered, the Allies knew, or should have known, that it was happening. The persecution of the Jews started years before, in plain sight. The United States refused to provide entry visas to thousands of Jews fleeing the Nazis. At the point when we could have done something to save those people, nothing was done. Whether we could have swayed the Nazis before the war started was moot; we didn't, and we didn't because the predominant political sentiment in the 30s was isolationism, and American anti-semitism was far from rare. By contrast Quakers in Germany worked quietly to save hundreds, if not thousands of Jews and other undesirables, without firing a single shot.
But maybe to bring that stuff is still dodging the question. Here's maybe a better answer -- as a pacifist, I can't deny the possibility that there is such a thing as a just war, but that doesn't justify war in general as a useful human activity. The first refutation of 'just war' is that there's no meaningful way to decide which wars are just. The root problem is that the human condition means never having any perfect knowledge. George W. Bush believes the War in Iraq is a just war. Most of the world does not. Bush is Commander in Chief of the most heavily armed nation on the planet, and has executive authority to attack whomever he wants, so we have his 'just war' going on and on.
My sister-in-law Tessa -- who was a freelance writer in the former Yugoslavia during the troubles in the 90s -- is in general a pacifist, but supported NATO intervention in Bosnia-Herzogovina and Kosovo. I don't necessarily disagree with her -- the Serbian nationalists were (and are) every bit as nasty as the Nazis, and the world needed to respond. But once again, the world waited until it was too late for a lot of people, and as always, it involved the incidental killing of many non-combatants.
As a pacifist, I have to acknowledge the challenge that WWII and Kosovo are to the idea of absolute pacifism. But that doesn't mean that trying to avoid wars and promote peace isn't practical. There are many non-violent, constructive ways to resolve conflicts, and in every war during my lifetime, it is self-evident that the non-violent means were shirked. War is an expression of the natural state of human beings -- xenophobic, short-sighted, agressive and selfish. Pacifism appeals to a drive that's a lot quieter in the human psyche -- altruism, compassion, and humility.
Since we've reached the point where our actions can exterminate all life on the planet, making peace is the crucial enterprise of all mankind. What would the world be like if all reasonable people thought that war and violence were an absolute last resort? We still need ways to protect ourself from the unreasonable, but there are ways short of destroying someone's country and thousands of innocent bystanders to try and bring them to reason.
You can point to the Nazis as an unambiguous example of an evil that justifies war, but if so, it only justified that war. It is instructive to look at the history of the last 25 years. The only countries in which formerly totalitarian governments have been replaced by effective democracies are the ones where an indigenous non-violent movement stood up to the bullies and said "you can't kill us all." Even in the former Yugoslavia, the only thing that really put an end to a murderous regime was a non-violent revolution. And what about South Africa? The ongoing nightmare of Apartheid only ended when both sides renounced violence and sought reconciliation.
Non-violence is slow. Violence is quick. Non-violence is complicated, Violence is simple. Non-violence is an ongoing, painstaking process, not an instant solution for human cruelty and violence. Non-violence means being willing to talk, even to those you perceive as an enemy. Anyone who says pacifism isn't a realistic moral stance is saying some things I find bleak and disturbing: that there are irredeemable people who it is a good thing to kill, that it's easy to see who the irredeemables are, and that there's no real hope for peace in the world. The first statement is in conflict with every human system of religious/moral belief, the second asserts, unrealistically, that human perceptions are perfectly reliable, and the third expresses pure nihilism and despair.
You can't say pacifism won't work because it's never really been tried. Let's give peace a chance, and see what happens. Even if pacifism fails, the failure mode for pacifism is war. We already have war, so what's the downside of trying peace?