You could write an entire thesis on this philosophical question. If you were writing a novel and I were your editor, this would be the topic of many long discussions.
I think there is no way to guarantee how a reader will react to anything you write, good or bad. Moral relativism aside, any individual is going to have their own set of feelings, historical awareness, educational exposure, and moral judgement they bring as your audience.
Many people consider The Handmaid's Tale (TV version) extremely dark, yet they still derive entertainment from it, perhaps because the dark elements are necessary to the plot, the character development, and most importantly, the social commentary of the story. Darkness or extremity are not necessarily bad. I depends on what you're trying to achieve. If you want a light, fun story or something aimed at younger readers, obviously those elements have to be toned down. Otherwise, it's a matter of personal preference whether someone likes the material or not. Gratuitous and excessive violence and cruelty are generally criticized as hack writing, though.
Cruel and unusual punishment and slavery are likewise difficult topics, as you noted. If you want to write historical realism and those elements are part of the culture, I think you have to acknowledge the reality. Truly good historical novels require a ton of research. I believe most adult readers understand that history has a lot of really terrible injustices, but ignoring those elements or whitewashing them is irresponsible because it denies the suffering of real people who lived through it. Your challenge as an author is to work with historical reality through a contemporary lens and with the benefit of hindsight.
I'm curious why are the main characters all "ok with it"? Is no one conflicted? Are they just implausibly oblivious characters? Are all the main characters in positions of privilege? Are they Ramsay Bolton level psychopaths? Why is theirs the only perspective of events? This already assumes a certain moral attitude. In every culture there is a mix of opinions about the status quo. It's lazy or misinformed to assume that because slavery was widespread throughout the Roman world, for example, that everyone was totally blase about it, or that everyone had the same idea of how slaves should be treated, what level of violence was acceptable as punishment for various infractions, etc. Those types of tensions in society are background elements in a story themselves.
The moral stance of your characters and the third person narrative is up to you. Having an event in your writing, like a slave auction, an execution, or torture, is not inherently problematic. Anything that is part of history shouldn't be taboo. The hard part is writing in a way that doesn't trivialize suffering just because it was acceptable and legal behavior for the aggressors.
Your question was fairly vague though I think you have a valid concern that is only going to be useful to discuss in specifics with an editor once you get some concrete ideas written down. Any advice at this point is likely to be wide of the mark.
The only general advice I could give is to consider the perspective and experience of all the people in a given situation. I think your question demonstrates understanding of why people might be offended by a society of legal slavery seen only through the eyes of the slave owners and never the enslaved people. Or by the culture of the enslaved being portrayed as uncivilized and barbaric, as per the bias of the slave owners. Don't fall into lazy cliches or tropes based on offensive outdated stereotypes.
As another piece of pop culture reference, consider how slavery and cruel and unusual punishments are part of the story in Game of Thrones. Maybe you haven't seen the show but I assume you have some familiarity. Think about how various fantasy cultures are portrayed and how they are perceived by their neighbors. Do some people delight in violence and others abhor it? Does the fall of the great empires built on slave labor carry an implied moral lesson? What do the various religions say about slavery and violence? Do their followers actually obey those moral rules? Why or why not? What happens to those who resist? How do the powerful and the weak fare in society? How do people criticize the establishment? (If you have no idea about this show, ask similar questions about some other scifi/fantasy books or films/tv you are familiar with.)
If you want to write in a fantasy universe, or a fantasy version of history, that requires even more layers of world building. Inventing cultures with histories of their own is a lot of work. Something like Game of Thrones has many elements of real history that the author draws on for inspiration. The original novel of Handmaid's Tale was notably written using only atrocious behaviors that really happened. Reading a lot of other authors and considering how they approach your questions is a good start. Think about what you admire about their stories and where they may have failed. Even something like TV Tropes (the website) can give you some ideas, at least of what to avoid.
Consider how and why you chose to incorporate those "dark" elements. Is is just gratuitous violence and cruelty for sensationalism? Or is it necessary to understand why a character behaves the way they do? How do you write the scene? Do you revel in the gory details? Whose POV do you give the readers?
Lastly, it's always a good idea to get as much feedback as possible in the editing stage. Try to get as broad a set of readers as you can so you get a range of perspectives. This sounds like an ambitious project - good luck!
