Yeah. Like in every totalitarian regime, the troops in Nazi Germany were heavily indoctrinated. SS were certainly the worst of the bunch, but regular Wehrmacht was pretty "Nazified" too. Especially those on the front lines, usually in such regimes anyone with a shred of conscience would be relegated to some backyard duties and stuck in low ranks, while any advancement would require greater and greater devotion to the ideology. Also, refusing to commit an atrocity would usually result in a death sentence, too, and I'm pretty sure many of them did all those horrible things just to stay alive. It's no different from other totalitarian regimes, really. People who had guts to stand up to their commanders existed, but were few, far between, and most were killed for that.
In fact, perhaps the only relatively Nazi-free service was the Kriegsmarine. This was shown quite well in Das Boot, IIRC, it only had a single Nazi party member, and he wasn't really a liked person. But then, Kriegsmarine wasn't really required to do a whole lot of this "atrocities" thing. Perhaps the worst thing they did was attacking hospital ships, but it's not like other navies didn't do it, either (not that it makes it any less of a war crime, but both sides are equally guilty of that one...).