I always took John and the other Spartans to be like Dr. Manhattan. Ozy says in Watchmen, most people can't see his emotions, so they think he's a unfeeling monster. He can see the subtle emotes, so he knows how to manipulate him. People consider them broken because they are a warped different humanity than they've ever seen. The only person who understands them is Halsey. I felt like Bungie, Nylund, 343 were going for this thematically, but I can't tell what they're going for anymore. Writing them off as broken, indoctrinated fools does little service to them as beings of choice, which Fall of Reach makes very clear the Spartan program was their choice.