This thread does appear to have derailed somewhat into chaos, but as we all love chaos and its much better than people killing eachother over whether their morality or the others is the better one I'd say its all for the best.
The quote at the start is the first one I thought of when I read the subject for this thread, as the Agent in Serenity is working to make a better world, however that doesn't mean the world he's helping make is better or even if such a better world would be created by his actions, just given blind obedience and the faith that it will.
Also on the subject of alignment with intent to do good through less than good means, I'm curious where Havelock Vetinari would fit in. I'd say somewhere between lawful neutral and lawful evil myself, as he is after all a Tyrant, and he gives everyone a choice. "help me do this and stay to hear me out, and at any time feel free to leave via the door over there. I won't detain you" However he also won't mention to lack of a floor on the other side of the "freedom" door. Fair but evil, but also neutral as he's offering life with benefits and a chance of redemption, or death and oblivion.
He's working towards progress and advancement for the city he rules but his methods are not always "good" by normal standards, I mean he's used slavery and other means, and the only reason he's not chaotic is that its a waste of time in his eyes and would lead to complications, hence why he legalised crime and put it under government control and taxed the populous so they wouldn't be mugged, and the muggers would track down and "remove" anyone who did mug someone who'd payed for their protection.
Also as far as he's concerned all mimes must be killed without hope, everyone has their quirks I suppose.