Nyar is an antagonist from the perspective of the Divine or Humans, but they're beyond concepts of human morality, like Cthulhu. You can't say an orange is evil because the orange doesn't understand what an evil is, except replace ignorance with knowledge and a perspective far beyond humans.
However antagonist is different than "Villain", as Villains are inherently "evil, living obstacles fighting the Hero", whilst Antagonist vs Protagonist is "An obstacle" versus "The viewpoint of the story". In that case, I'd say the OCs are the obvious "Viewpoint of the Story", so I believe it follows that dynamic rather than Hero vs Villain when it comes to beings such as Cthulhu or Nyar.
In that respect, its impossible for Nyar to be the "main" villain, but they can be a primary "antagonist" who opposes the "protagonists".
In my opinion we should just have primary villains rather than a designed evil guy and see where it goes from there. I don't think we should flood the RP with Villain characters though, or this is going to become a lot less about a growing evil and more like an immediate civil war between the Gods with little build up.