Introduction
I have heard it argued that there is no meaningful way to compare atrocities; that the murder of one man is so horrible that it cannot be countenanced in the pursuit of any end; and that therefore any atrocity in wartime destroys the legitimacy of that combatant.
An Impractical Standard
The problem with this is that a moral standard, to be meaningful, must be useable as a guide to some action, or away from some action, which can be accomplished in reality. If I propose, for instance, that it is immoral to possess mass because one thereby forces the worldlines of others toward oneself through gravity, this is a meaningless moral standards: we are all made of matter, all matter possesses mass, all mass possesses gravity. At most this would be an argument for dieting.
Now, war is an inherently destructive and violent business. While a combatant should certainly attempt to hold the number of atrocities committed to a minimum, the fact is that all barrels contain some rotten apples, all humans are imperfect, and when armies of hundreds of thousands are put in the field, some persons will through malice or mistake harm innocents.
If we apply the "any atrocity degitimizes the cause" standard, then all armies will find their causes delegitimized, because all armies will commit some atrocities. This may be praised as a declaration of moral rectitude; but it has the opposite effect.
You see, if we hew to this absolute standard, all armies are equally guilty: this includes the most honorable regiment no less than it does a barbarian horde; the American GI's no less than the German Waffen-SS troopers. This also means that no army can be judged any worse than any other, and hence that there is no reason to even TRY to prevent atrocities.
Clearly, this standard does not work, in the real world.
So, what alternatives can I propose?
Size Does Matter
Those who know history look with horror at the Assyrians, the Mongols under Ghengis Khan, the Germans under Hitler, the Russians under Stalin, the Chinese under Mao. Why is this? Because these nations, in making war, slaughtered immense numbers of innocent civilians; far more so than was the norm under the Rules of War in the ages in which they operated. If killing one innocent man is bad, clearly killing a hundred or a thousand or a million such men is worse.
We can judge this in absolute or in relative terms: both are useful for various purposes. Absolutely, it is terrible that Mao murdered sixty million people (some in war, others in peace). But of course some of this magnitude was due to the fact that he ruled almost a billion souls. Lt. Calley's company behaved quite atrociously even though their victims could be counted by the dozens; this is because Calley commanded far fewer men than did Mao.
One must logically consider the size of a force when judging atrocity: an army of a hundred thousand which defeats an division of ten thousand and in the process of taking prisoners captures five thousand but shoots twenty men attempting to surrender has, by and large, obeys the Laws of War; a platoon of thirty which induces an enemy squad of ten to surrender and shoots all ten of them in the process is not, even though it has killed only half as many men.
This sounds cold and terrible, but such is the nature of war. People die, some die wrongfully, and one cannot compare the severity of such wrongful deaths unless one is prepared to compare numbers.
Cruel Intentions
Those who should be spared sometimes die in war; this may be deliberate or accidental. There are degrees of deliberation.
Shooting a POW who is in a prison camp under your control is worse than shooting one who is being marched back to the rear; which is worse than shooting an enemy soldier attempting to surrender. Deliberately lining up and machinegunning civilians is worse than accidentally shooting them because one mistook them for enemies in the field. Intentionally firebombing a residential district of a city is worse than hitting one with stray bombs when one was aiming at military targets. And so on.
Again, these sound niggling, but making such niggling distinctions can literally mean life or death for the innocent. "Rules of Engagement" attempt to make such distinctions ahead of time; carelessly formulated Rules of Engagement can lead to much suffering for the innocent. Sufficiently bad formulation of Rules of Engagement, by the High Command, can count as a war crime in and of itself: witness the orders given by Stavka when the Soviets were conquering Germany in 1945, and their effects.
An atrocity committed in accordance with cruel Rules of Engagement, or at the command of high-ranking officers, is generally considered worse than one committed in defiance of humane Rules of Engagment, or at the comand of high-ranking officers. This is because the higher the rank at which the atrocity is ordered, the more it reflects national policy. Armies do get out of control, as witness the Sack of Badajoz in the Napoleonic Wars (in which the British troops raped, pillaged, and murdered allied civilians, which was not a reflection of national policy!
Severity of Harm
This should be obvious, but not all atrocities involve equal harm to the victims. Aggravated murder is worse than simple murder, murder worse than rape, rape worse than simple assault and battery. This is generally formulated in an army's martial law; ours is called the "Uniform Code of Military Justice," and treats those guilty of war crimes rather severely by most historical standards.
Sanction
One must, finally, judge the side by how it treats those responsible for the atrocity. Most Western combatants consider atrocities crimes, and prosecute them. Many combatants don't really care about atrocities one way or another, and make no effort to punish those on their own side responsible for them. Some combatants (the PLO and Al Qaeda come to mind) consider atrocities laudable, gloat over them, and reward those responsible.
Conclusion
The commission of atrocities in war is a serious matter, which is why they must be seriously and logically judged, so as to render such atrocities rarer in future conflicts. Using the claim of "atrocity" as a moral club to beat a side of which one disapproves may be emotionally satisfying, but out of context does worse than nothing to solve the problem.