The Sonderkommandos and Einsatzgruppen that carried out atrocities against the civilian population were small volunteer-only units.
Throughout modern history it has been recognised by all military commanders and theorists that permitting or encouraging the troops to commit atrocities is bad for discipline, morale, and overall fighting quality. And the corrolary is that it is usually the very poor quality troops who commit atrocities. For example, much of the rapine committed by the Soviets during their advance through the Reich was the fault of inferior, rear-echelon troops, NOT of the front-line Red Army. Or at least this is what I have heard. And I am generally willing to give the Russians the benefit of a doubt.
In addition to "genuine" atrocities against civilians, there is a make-believe class of atrocity -- the type for which Kurt Waldheim stood accused, if I recall correctly. That is anti-partisan warfare, now called "asymmetrical warfare." There were SS units involved in this, often recruited from the local population. This meant that pre-existing local feuds were incorporated into the "war currently in progress." So the Germans supplied one side, and the Russians/British/Americans supplied the other side. And both sides employed the same brutality that they always had. But since the Germans lost, they got to play the role of war criminal during the show trials afterwards.
The U.S. got a taste of asymmetrical warfare in Vietnam. And England did in Ulster. And Russia in Chechnya. All of these victors of World War 2.0 committed acts that would have been criminal if subjected to the same criteria used at Nuremberg. I would also point out that the IDF is now engaged in anti-partisan warfare that entails frequent collateral damage among the civilian population.
One would think that these more recent lessons might lead people to understand that the line between anti-partisan warfare and atrocity is quite blurred. But it apparently isn't, because there is no end of people who are willing to mount the PC soapbox to hold soldiers of the Third Reich to a moral standard straight out of King Arthur's Court, while nonetheless making every possible allowance and admitting every conceivable extenuating circumstance for "our boys." Even more "troubling" (to borrow a term from Abe Foxman) is that we are now expected to hold the children responsible for the crimes of their fathers. I will limit myself to pointing out that this is not a particularly "Christian" attitude in an ostensibly "Christian" country. But perhaps our traditional ethics have been supplanted by something quite different.
Now, getting back to my first statement . . .
In certain circles, to even suggest that the majority of the Waffen-SS (and, it goes without saying, virtually the entire Luftwaffe, Kriegsmarine, and Heer) were innocent of warcrimes is to make one a neo-Nazi. This opinion, however, is prevalent among ALL military historians, and is still to be found among serious military books and articles, as opposed to the "Why We Fight" mentality that has been revived in the popular media.