The Operative was completely stone cold sane. He knew that he had to do horrible things, that he wasn't a nice person because of those things he had to do. But he had such belief in the rightness of his cause - the Alliance - that he considered any unpleasant means to be worth the end. He did the things he did because he wanted the final result for the entire known 'Verse, even if he himself was not allowed to be a part of that 'Verse because of the things he'd done to achieve his end. In short, he was a true believer, not a paid mercenary.
That's a very interesting perspective. It makes the Operative a lot like Sloan on DS9
. But Sloan had Bashir as the the perfect foil, whereas Mal is no idealist. Which leads me to the problem:
And that's important for the story, because at the end of the story the Operative loses his religion.
Sloan never has an illusions that the Federation is doing bad things, because he's
doing bad things. All the time. In order to save the Federation, which he believes - however flawed - is fundamentally good.
That's why I don't believe that someone like the Operative could lose his religion at the end. The man has done some horrendous shit in his life - just in the opening minutes he slaughters the lab staff that let River escape. It seems unreasonable that a man who has seen as much as he has - who has done
as much as he has - would be shocked by the Reaver reveal at the end.
Sloan wouldn't even bat an eye.