In my story we follow a group of brave soldiers who strive against a numberless enemy for the good of their nation. They fight hard to save the people of their city, and are willing to sacrifice their lives for their country. They also believe in the collection and conscription of 'sub-humans' for use in war. As they rescue their population from the invaders they gather criminals, the mentally infirm, addicts, homeless, and the infertile for categorization. These oppressed people are given the 'honor' of being shipped to the front lines where they are can earn proper rights and citizenship through serving in the defense of the very country that labels them as 'lesser'. As a final insult, the oppressed are given false memories of their pasts. They are brainwashed, led to believe that they are all criminals, and that their fight is a struggle for their own redemption. The nation's actual soldiers try and guide these people to success, and view them as brave and noble. They will soon be 'real' people, anyway. However, most soldier believe in the use of these conscripts, and think that the brainwashed people are getting a good deal. We get one small view of sanity when some outsiders comment on the horror of these acts, but for the most part we are with the soldiers as they fight alongside their noble 'subhuman' comrades. They talk about the burden of caring for these poor, confused people, and the danger they present on the battlefield to 'real' soldiers. How would you frame, write, describe this sort of dynamic? My plan is for the 'undesirable' soldier to figure out what is going on, and start to question their orders, comrades, etc. Despite this racism and slavery, I am writing the story in a way where you are supposed to care about the soldiers, despite their abhorrent behavior. The story primarily follows a victim of these acts as they try to earn their freedom through this twisted scheme, but there are also 'evil' characters that we are supposed to worry about. At the very least, their death will make things harder for our hero.
It's simple. Give the "superior" soldier likeable personalities and make it clear the believe in their won goodness. I mean, they're already soldiers, these are people who are trained to fight and potentially kill. So having them be more accustomed to darkness is actually kind of expected. It's easier for them to take a hard view of morality that focuses on ends rather than means.
Part of getting Iraq under some resemblance of order involved either rebuilding or creating from scratch, local and regional police and national guard units. Identify a wealthy or powerful family in a community, hand them a catalog for uniforms, vehicles, weapons, and supplies, then cut them a check. Wealth and power found other wealth and power to be in charge. If someone was an actual police officer, or national guardsman, they were likely poor, displaced, or their version of a serf. As a rule, they were terrible. They were not bad people, and we did not treat them poorly, but they were under-trained, not well enough equipped, and had completely different sets of motivations that might or might not fit with what they were being asked (or paid) to do. Some were okay. Some did really well. Some were just ineffective, some were unintentional dangers to themselves, some were unintentional dangers to American soldiers. Because they represented American interests, they wore targets on their backs, and many died because of that. And because we wanted them to take responsibility for their areas, we asked them to do things that put them directly in harms way, asked them to put their lives in danger so we did not have to, and many died because of that. We all saw the process as necessary in order for us to go home and stay home, rather than come back every other year for the foreseeable future. Is that a shitty comparison? I don't know. This is where my mind went. Certainly what you are describing is at least one order of magnitude greater than what I am, but assuming my comparison is even remotely relevant, would you consider the actions of the soldiers as abhorrent? As separated from the policies themselves? So I guess to answer the question, how do you write that, would be to write the soldiers as performing a job, doing their duty, given the tools at their disposal and the circumstances they exist in. Let the reader determine the morality of the situation as they will.
Some of these seem fairly easy to hide, which invites the possibility of a "subhuman" PoV character who hides it and serves in a regular squad. They'd have a very different perspective than other PoV soldiers who have nothing to hide.
Try infusing the morals of equality between the soldiers and the 'sub-humans'. They're all fighting a war, so the fact that they're fighting together leads to a kind of unity. Unity through strife. As time progresses and the subhuman discovers what has happened, he can be 0pen to many avenues of interaction with the real soldiers. Do they trust them like they in turn are trusted? Does he believe they are involved with it? Does he tell them? If he does, how do they react? There's a lot of directions you can take with that, so your story is open to a lot of avenues in terms of what you would want to convey.
Action heroes are able to get away with countless atrocities without the audience batting an eye. Portray them as cheesy self-righteous heroes initially and slowly reveal the reality of the situation. This would actually be a great setup for a satire on action hero protagonists in fiction and/or the United States's over-glorified military.