Dead Boys (Coalition soldiers) in Rifts. The typical grunt soldier is a perfectly normal person when he's not slaughtering villages of helpless aliens or shooting mages in cold blood. The sad truth is that they've been indoctrinated from birth to believe that all aliens and magic constitute a very real threat to them and their loved ones. It never occurs to most Dead Boys that they're killing people just like them, with hopes, dreams, and their own families. Most of them can't even read (the Coalition States have a strong anti-literacy stance), and thus have no way to learn anything but what the Coalition teaches them. They are generally used as stock villains in Rifts games set in or near Coalition territory, and they do commit rather horrific acts.
It's explained by fluff that many of the "bad guys" in Warhammer 40K are actually just this trope; common soldiers obeying their commanders, many times not even aware that their commanders are in open rebellion if not outright Chaos cultists. It's even worse in some of the larger ships in the Imperial Navy, whose populations can match those of small countries; entire generations live and die on them, some not even leaving assigned areas, and are so conditioned to obey orders that they neither know nor care whether they're subduing a group of heretics or virus-bombing a pacifistic pre-industrial society.
The Wyld Hunt (sic). They oppose the Solar and Lunar anathema (that is, Player Character) not out of personal grudge, but because it's a job that pays. Although there are some who take it a bit over the top.
Usually if the Guild is involved in something bad, there's no malice involved, it's just business. Very ugly business, sometimes - drug dealing, slave trading, assassination - but still business.
A hefty percentage of Alpha Complex's population in Paranoia.
The Balance and most of the shrouds in Anathema don't enjoy murdering millions (or even billions) of people or have a personal vendetta against their victims. They do it so that the planet won't be rendered uninhabitable by overpopulation.
The Seers of the Throne in Mage: The Awakening are an example of this being played straight for horror. They're mages who've chosen to serve the Exarches, the god-like Supernal Symbols of Tyranny, because A: they've won, B: it's easier than fighting the status quo, and C: it's an easy route to power. There's usually very little personal dislike for the Pentacle Orders, the Seers are just Selfish Evil to the core.