The idea is, of course, that most of the lives we take are really evil anyway, so we're actually doing the real good guys a favor. We kill tons of demons, ghosts, zombies, dragonkin, giants, and rabid beasts -- even most of the humanoids we kill are bandits or wicked cultists of one sort or another. This way we do lots of killing, but still feel as though we are heroes.
There are some situations in the game, however, that turn things around for us, in which our character is not the hero. While there are some higher-level instances such as the Black Morass, or the new Caverns of Time: Stratholme, in which one could argue either way whether what we're doing is good or evil, most of situations in which you are clearly the bad guy, as far as I am aware, have to do with the undead, and to a lesser extent the blood elves as well. Of course, you can argue that in general, undead are just misunderstood, and the blood elves are just tragically misled, but as in the case of quests in Hillsbrad that ask you to go slaughter human farmers, or help develop a new plague, there's really no denying that your character is doing something "morally wrong."