[I'm kinda busy in real life, so I'll reply and log off again. Maybe I can check back in 15 min, maybe it will take 4 hours... Who knows? Apologies in advance]
Before I tell you of a possible scenario I thought of when I read Habis's last message, let me repeat this: as Orchis has been described so far, as an organization, I can't really present them as morally grey either.
But I'm still curious in case someone can! :)
Now... as an individual antagonist, being the leader of a smaller conflict against Krakoa? Yeah. I think it could, in theory, be done.
Imagine a person has a problem with Krakoa's policy of diplomatic immunity to all mutants. Imagine this person, for whatever reason, is truly compelled to do something about it. They try every way they can think of (including trying to talk to mutant ambassadors and heroes) without avail. Eventually, they come to the conclusion that Krakoa will not change, so the problem is the Krakoa nation itself and the only way they can actually fight existence of Krakoa (not the existence of mutants) is to join Orchis.
Now, perhaps this person is not seeing other alternatives because they're exhausted, perhaps they were always too desperate to be able to see it (depending on what compelled them to act in the first place). It doesn't matter. What matters is that they got to that conclusion.
Here is the thing. If this individual started as a morally sound person, they'll become, at the very least, morally grey at the moment they actually join Orchis. Because, sure, even if they tell themselves they'll only be using Orchis' resources to help take Krakoa down and nothing more, they have to know Orchis will most certainly not stop there. A person with a good moral compass would not think this is the lesser of two evils.
A person with a good moral compass sometimes is able to lie to themselves, though, so they can do something they despise. It still harms their morals, but they'll keep telling themselves they're justified (and that, if well executed, could be gold by itself).
So there we have it: a compelling antagonist who one could argue is evil by association, but who doesn't want to kill or enslave mutants. Someone you could understand the motivation even if you disagree with their perspective and their methods.
Is it possible to write such a story? Yes. But it's very tricky. I suppose it's easier to execute it in a novel. Only a very good comic book writer can pull this off using the comic book medium.