To Ocelot's defense, he did want to bring Quiet back alive because he saw the potential in her; the potential to kill and slay more enemies. So while he's not being the twirled mustache badass we're used to see, he was facilitating Snake a way to get rid of more soldiers.
Maybe Big Boss is an evil bastard, but personally, I can't identify myself with Solid Snake even if he's a hero (something he didn't want to get known himself). He seems too cold, too calculated. Less... human. I think that is a point that devs subtly wanted to insert in the series. I'm not saying that Snake is less of a person for being a clone, but he's a government tool to make a wet work. He even said it himself.
I wanted to share something a friend passed me last night. http://m.imgur.com/qUHXy5n







