I was talking less about the institution and more about the intersections of convictions and methods. Now take that and examine how that intersection influences whether we view Butcher as a hero or anti-hero.

That's a pretty fine line. Butcher isn't the protagonist anyway, which is good because he's the weakest aspect of the story. He hurtles from one situation to another, bringing no resources of his own other than a generalized ill humor. Some CIA bureaucrat bails him out today, a long-lost aunt cheerfully abides the total destruction of her neighborhood tomorrow, a rando schlub turns into the James Bond/MacGuyver hybrid he needs next week. Plot armor is not meant for deuteragonists; Butcher should definitely have been killed off sometime in second season.

Sorry, what? I do not know how you can consider Butcher not a protagonist.

Hughie is the protagonist. The viewer and nearly every other character relate to him and his actions. Butcher OTOH is a violent inconsiderate weirdo who is hated by everyone, including his parents. (He is barely tolerated by those he has dragooned onto his "team".) Butcher was convenient for getting the action started but after he transitioned from "mysterious stranger" to "surrogate father" to "everyone hates this asshole", his role would have been better filled by others on the team.

It would be a considerably more "experimental" program if a character like Butcher were the actual protagonist.