Can you clarify what you mean by protagonist-centered morality? I think the show does a pretty good job with moral ambiguity and showing different sides of issues. The recent events with Bismuth and Jasper have made it pretty clear that both characters are meant to be sympathetic, despite respectively being an antagonist and fundamentally disagreeing with Steven/Rose's approach to the war. Plus there's the fact that Steven himself does try his best to understand and empathize with his enemies, even when they're straight-up trying to kill him.