I am not saying that slavery is good. It is wrong, but what if it isn't wrong in your own fantasy world? If people are going to be stubborn, then I guess all stories need cliche' morals about what is right and what is wrong.
So you're saying you're trying to create a hypothetical situation where it wouldn't be wrong, or at least would be the best of many possible choices?
If so, the burden of evidence will be very much on you as a writer, and you'll still probably lose readers who are inclined (through their own background and experience) to empathize more with the slaves than their masters.
But this sounds like you're trying to write a story with a moral too, even if it's just "Look! Slavery
could be the most ethical choice if [insert fantasy scenario]."
If the main character has a slave girl who he mistreats for his own pleasure, there should be a reason why he does it. Maybe he is a spoiled brat, or bullies treat him like crap, which makes him beat his own slave because he couldn't defend himself. Then maybe his slave tries to help him. Complexity.
Yes, complexity and reasons are good. Maybe he even just does it because having absolute power over another is in of itself corrupting, and he's never known anything else. Every character should have reasons for doing what they do.
And I assume the slave is trying to "help" him be a better person so he doesn't abuse her anymore? Or maybe she's got a sort of Stockholm syndrome--the thing that makes people identify with their captors and abusers when they are the sole source of support/contact in their lives. Or maybe she's lived as a slave all her life, and she knows nothing else, so she believes it's her duty to love and help her master (much as abused kids often still love their parents or battered spouses are conditioned to love their abusers and think there's a way to exert control over their situation by changing their own behavior). Or maybe she's more cynical, and having such a high-status master gives her enviable standing with the other slaves, and being loved by such a master makes her position more secure.
Complexity, as you say. And this is something that's often missing from old-style fantasy where slavery and other unsavory institutions existed as window dressing. What did the victims feel, and how did they maintain their own sense of control and/or dignity?
And yes, of course some people will be kind to their slaves and some won't. That's the range of human behavior one sees when someone has rights over another, and social pressure makes a difference too. Just like some people hurt or neglect their animals in our world, and some don't. Just like some people hit their kids and some don't. And there may be laws or customs in place that place limits on whether or how hard masters can beat their slaves, just like there are laws that dictate how parents may discipline children (or laws dictating what we can do to animals). And you'll have to decide how those laws are enforced in your culture, or whether they really can be.
A big question in any slave-owning culture, I'd think, is how people exert their control and rights over other adult people who may be just as smart as they are and are likely to have reasons to become lazy, disagreeable or disobey, at least some of the time.
In a SF scenario, you can invent a technology to do this (in CJ Cherryh's universe, aberrent or unhappy Azi are given tape to "calm" or "reeducate" them," but in severe cases they are "humanely" euthanized with the same kind of sadness with which one might put a sick or intractable animal to sleep. In a magical world, is there some kind of magical control or coercion? Or is physical force or punishment warranted and allowed in some situations?
I can't really see a way of portraying these things that won't be sending some kind of message and make people uncomfortable, however. Again, if you don't want to raise uncomfortable questions that will make your readers think and feel uncomfortable things, then you need to leave uncomfortable things out of your stories.
And yes, as KN says, anything you write will bother someone. The point is to be aware of what you're doing and why you're doing it. Offend the right people for the right reasons.