Maybe, but the way I'm seeing it is that in those games, the setting is "modern and realistic" but the story has elements which are not very likely. Still, because of the "modern realistic" setting, the characters can be judged according to the player's mindset.
It's the flip side of a "modern and realistic" setting. We will judge the characters according to our own moral/personality. This while with all the other settings, even "modern and unrealistic", we tend to be more tolerant because it's not "our world".
By example, outside of all fetish, a rapist character will be less likely welcomed on a "modern and realistic" setting, than on a "sword & sorcery" one by example, because we'll think that "at this time it was the norm".
For instance, Luna is on one hand a murderer but on the other hand also sweet and innocent. One thing we perceive as negative the other as positive, thus creating character depth. But this perception is only possible because of the setting. In a setting where murdering is fine but innocence is frowned upon, Luna would/should be seen in a completely different light.
I think that you don't need to go as far as changing the setting, changing the context is enough.
Put Luna as everything else than the daughter of a head of a Mafia family, and her complex and deep personality will be limited to a freak one. In fact, it would just not works. Outside of this context, you can't be both a cold murderer and effectively a sweet innocent girl ; unless the context is perpetual war, yet the said war have to really be perpetual, the character need to know absolutely nothing else for her personality to keep its realism.
To go back to Dune: I personally find the Bene Gesserit a thoroughly evil and wrong organisation.
For me, they are the Nazi party of this part of the universe. They don't use (directly) violence as a way to achieve their goal, but their goal is to purify the race and create the perfect "human".
But in the setting of the novels, they are not always seen as such, with many of the "good" characters being members or being allied to them etc.
It's, from my point of view, the most marvelous idea that Herbert had. They are all women. Therefore, from the point of view of the reader, they can't be this bad, right ? As for the point of view of the characters themselves, they are their wives, sisters, mothers, daughters...
The Bene Gesserit is the most beautiful conspiracy of the Dune universe. While the head of the families use poison, murder and war as more or less discrete weapons for their conspiracy, they use blood relationship for theirs. No one can effectively goes against the Bene Gesserit without also going against part of his own family.
The Tleilaxu on the other hand I somehow find kind of sympathetic, but in the novels they are generally portrayed as the bad guys.
They are the one that gave up to their humanity. Add to this the fact that the Tleilaxu ask for money, while the Bene Gesserit don't do, and how can they be perceived otherwise that greedy monsters for the characters ?
But for the readers, the opposition with the Bene Gesserit goes further, because we have access to what is missing for the said characters, the effective goals of both. And, because the Tleilaxu's goal is at the opposite of the selfish goal of the Bene Gesserit, they become the good ones ; greedy, but working for the good of the humanity and not their own sole good.
Clearly my personal morality and that of the characters in the novels do not match. On one hand this is confusing, on the other hand it gives the worlds created in the novels a lot of additional depth.
You put your finger of one of the most, if not the most, difficult part of a good writing : The creation of this duality between the way the reader will see someone, and the way the characters will see him.
As I implied above, it's natural that your view on the Tleilaxu and the Bene Gesserit are at the opposite of the one of the characters. But to achieve this, you need to always keep in mind that people wear a mask and never are exactly the same in public and in private. And, obviously, you need to never mess with the two personalities that it create, not mixing them by error.
Take Luna by example. As player we know her sweet and innocent part, but ask anyone outside of the DeLuca family (and probably even most of the soldiers of the family) and I doubt that you'll find someone that don't see her as something else than a fucking freaks of murderer. This because
HopesGaming achieve to deal with this dual personality.
Luna is sweet and innocent when she want an ice cream, it's seen both in the dialogs and the CG. But once the two jerks come, it's finished, there isn't a single part of this that stay. And even when the said jerks are supposed to be outside of the scene, she stay cold and freaks in her attitude, but the sweet and innocent part come back in the dialog. She could have relaxed her attitude, but there's surely witnesses since she used her gun, so the sweetness part is limited to what only the MC can witness.