Pacifism is not the same as peace activism; not all peace activists are pacifists. The concept that violence may be necessary in certain instances is widespread in our society, and can be found in the peace movement as well.
Pacifism opposes violence thoroughly. This means that pacifists will not commit violence themselves, but also will not participate in other people's violence. Apathy or cowardice are every bit as disallowed as committing violence is -- because those attitudes allow for violence in other people.
As in this joke:
In the days of the old West, a drunken cowboy when charging into a saloon one day and waved around his Colt pistol, shouting "All right, all you mangy varmints, clear out! And give me some elbow room." As one, the assembled gathering arose and departed in great haste. But over in the corner was a man in a broad-brimmed hat sipping a glass of orange juice (we do have to account for what a Quaker was doing in a saloon). The cowboy staggered over to him and said, "I don't believe you heard me, pardner. I said for all the mangy varmints to clear out." The man looked up and replied, "I heard thee, friend. And I must say, there certainly were a lot of them, weren't there?"
Most acts of non-cowardice are more serious, of course, but this is the point: pacifists find cowardice or apathy just as repulsive as advocates of just-war doctrine do.
The current denominations with long-standing pacifist traditions going back hundreds of years are the Mennonites, Church of the Brethren, and Religious Society of Friends (Quakers). Many other groups have existed throughout history and in other religions besides Christianity. Common Christian practice before Constantine was fairly uniformly pacifist; the disciplines did not allow Christians to become soldiers, and men who were already soldiers who became Christians were allowed to remain (it was a death sentence for them to resign early) but only so long as they did not kill. The early Christians were also entirely consistent in spreading their opposition to the killing of humans across the board, since they also opposed abortion, infanticide, euthanasia, the death penalty, and the gladiatorial games (for which they proposed contemplation of God-created nature as a better spectacle.) Documentation of this can be found in the book: Consistently Pro-Life: The Ethics of Bloodshed in Ancient Christianity, written by Mennonite author Rob Arner. (Mennonites are officially both pro-life and pacifist.)
First delineated in a major way by Augustine in the 300s and developed much since then, the idea that there are "just wars" is a departure from pacifism – but pacifism is what it is a departure from. Wars of aggression are still regarded as outrageous; wars for territory or to respond to an insult or to get revenge or to turn boys into men are still out of the question. Only defense of the innocent is allowed as a motivation for war, and then under a set of strict safeguards.
The "just war" theory is therefore not the opposite of pacifism; it would be such things as mindless genocides that would be the direct opposite of pacifism. The idea of the "just war" is instead pacifism with exceptions.
Those who advocate the just war doctrine think that pacifists are naïve to think that there are not times when violence is necessary to protect the innocent. Pacifists think that just war advocates are naïve to think that wars can be done within the strict limits set. It's in the nature of wars to get out of hand. This is how violence works. Once violence has its foot in the door, it snowballs.
However, the debate actually matters very little. Pacifists would be delighted to see the "just war" limits applied, and in fact make frequent appeal to them. There has never been a war where one side has met all the criteria as a just war. It's very rare for one side to even come close. Allowing for human imperfections, the number of wars that would remain if the "just war" standards were loosely applied to one side would be so few as to make war rare, as the preventing-the-death-of-the-mother exception is for abortion.
The way violence works is that it starts out small and grows. This has been noted in history and there are sound psychological understandings of how that works. It's naturally far more difficult to deal with violence after it's gotten out of hand than when it's still at its small beginning stages. Therefore, pacifists in particular, along with other peace-movement people, will make a point of focusing on how to resolve conflicts or stand up against injustices while they're still small. It's not merely a matter of being picky. It's being conscious of nipping violence in the bud.
It would be the equivalent of having a large pro-life movement working hard in the United States at preventing the state laws that were allowing abortions back in the 1960s. With enough effort strategically applied back then, perhaps we could have avoided Roe v. Wade. This very dynamic has in fact worked when it comes to infanticide: by the time the results of Roe were working their way from feticide to infanticide, a large pro-life movement threw a fit with individual "Baby Doe" cases where children with disabilities were targeted. The partial-birth abortion bans have also put a halt to the progression from feticide to infanticide. And of course we're trying to do the same now with assisted suicide and euthanasia – and while there are many places we haven't succeeded, is there much doubt that we would be in way worse shape on this now if we hadn't been active?
This applies to many wars commonly regarded as "good." There's ample evidence that dictators from Saddam Hussein to Adolph Hitler were actually encouraged by the countries they were later at war with – and peace movement people in general and pacifists in particular were strongly advocating against this early on, when the problems were already obvious. Had they been listened to, major wars may well have been less bloody or avoided entirely.
A common argument against pacifism is the individual case, and a classic one is an insane person threatening the life of a loved one. But in order to work as an example, the situation needs to be stripped down to its simplest components. Such is the nature of violence -- it thrives on over-simplified thinking and withers with complicated reality.
Does this madman have a mother who will grieve his passing? Does he have a following that will avenge this death? Is he a police officer so that the weight of the dictatorial government will be coming down on you? Why is it that a person whose mental illness is so dangerous is out on the streets – has society done its job in restraining such a person? How was it you were able to ascertain quickly that he's insane – is he maybe drunk or high instead? Or simply off his medications and will be fine once he gets back on them? Has he recently suffered a trauma so that one quick distraction and a listening ear would solve the problem? Is he following habit, so that going contrary to his victimizing script would throw him off balance?
In any event, we haven't identified the actual need. There is no need to kill or severely injure the man. The need is for emergency restraint. If you're making preparation ahead of time for the contingency – after all, effective violence requires preparation as well – then surely non-lethal means of restraint are a better option. If this is a sudden surprise and you have no preparation, then there are still plenty of nonviolent tools that can work (or minimally violent tools, like tripping him).
And you'll be much better off with the nonviolent and psychological methods, because without advance preparation, the chances are high that the madman is better able to use violence than you are.
In an episode of Star Trek: The Next Generation, the Klingon Worf was in an accident leaving him paralyzed. According to Klingon tradition, this meant he should commit ritual suicide, and he was intent on doing so. The doctor was appalled. She tried to research Klingon physiology to find treatment, but Klingons had no advice to give. Since they always committed suicide on such occasions, they had no information. Various creative things were tried for allowing him to live and function with dignity without full use of his legs, and finally a procedure which cured him was found. Solutions could be found because the option of assisted suicide was out of the question.
Once a violent solution is on the table, it keeps alternatives from being developed. Violence as a problem-solving technique has the apparent advantage of being quick and efficient. We just ignore long-term aftermath. Nonviolent alternatives take more care, attention, resources and time. They have obvious advantages in the long run, but the short-term consequence is more work.
This leads to the ironic outcome that foreclosing an option means more options become available, rather than fewer. Pro-lifers, for example, have a much more extensive and complex set of services offered through crisis pregnancy centers, maternity homes, mentoring, and government social services than the relative simplicity of the abortion clinic. Some maternity homes closed down after Roe v. Wade once the option of abortion was no longer legally foreclosed, but many more have now sprung up as the option has been understood to be repugnant.
In the case of war, pacifists who by definition foreclose it as an option entirely have offered a wide array of ways of dealing with problems of conflict, violence, and injustice, including nonviolent conflict to achieve democracy and human rights. People inclined to resort to weapons are less likely to be creative in finding alternative ways of resolving problems.
Mohandas Gandhi, who once said it was as clear as daylight to him that abortion would be a crime, put it this way: violence is only "necessary" when the nonviolent alternative has not yet been discovered.