But... SU doesn't really have protagonist-centered morality? Certainly not by the standard definition, which would be "Steven does bad things and gets forgiven for them because he's the protagonist." He tries his best to be kind and understanding to everyone he meets, even the antagonists, and sometimes that works out well (like with Peridot), sometimes it works out poorly (like with Jasper and Eyeball), and sometimes it just complicates the situation even more (Bismuth, Lapis, and arguably Centipeedle).

Steven does still see the world in a kind of black and white way, but he's a kid, after all. He's inherited a 5000 year old war from his mother, and there's a lot he doesn't know. Season 3 has been all about learning the things he didn't know and how he reconciles that with what he thinks is right.