To black spider I agree to this in the real world. but where do you draw the line in the real world. Killing flies, spiders, mice, sheep and cattle. (1)
But in a game why not be the bad guy during that bad guy quest then switch back to being the good guy again.(2)
I play the game as the good guy only killing when attacked by others but I still accepted that the dark brotherhood was just another part of the game and just went along with it.(3)
Regarding part 1, I draw the line in the real world when you kill animals in an inhumane fashion or when you're killing people that shouldn't be killed. I've got no problem with Osama being assassinated and while I think the Israelis are occasionally overzeleous, I don't really have a problem with an attack helo being used to take out known terrorist leaders, even if they are hiding behind women and children. Some times the hostages can't be saved and sacrificing them is the lesser evil. I also don't have a problem with the death penalty for particularly nasty crimes when there's no doubt whatsoever about guilt, at least not in theory. In practice I find it intolerable that mistakes can happen. You can let someone out of a prison but you can't resurrect someone who is already executed.
Generally, I place human sustenance above animals' right to life and I don't put too much value into the rights of violent criminals, though I do put great value into not punishing the wrong person. Since the "wrong person" can go to prison, the idea of treating prisoners like human garbage doesn't work well with me, and since the accuracy of convictions could be greatly affected by the government of a country, I put value into the concept of civilized and humane punishment of all criminals, even those who don't actually deserve it.
Regarding part 2, I have to say that either your character is good or he is not. Being good means doing the right thing because it's the right thing, even if it comes at a price. You can't join the thieves guild unless you can justify how stealing from other people is "good". You can't get the black star. And obviously you can't do DB quests because being a hitman just isn't "good". There's also a number of Daedric quests you have to refuse, fail, or stay away from. That's being "good".
You can also be grey in various shades. For instance, you could be sort of light grey and borderline good without actually having the moral sentiment required to be actual good. Think of it as "honorably neutral". You care about good and evil but you also care about yourself, since you can't do much good if you're dead or dirt poor. Even so, if you have options then you prefer the good option, unless the evil option is not too evil and pays a whole lot better.
Of course there's also the dark grey version of the above where you care very little about laws or rules and do what benefits you, but still without the complete self-devotion and lack of empathy that characterizes true evil. You don't mind screwing over random people, you don't mind making them starve a little bit, but it doesn't bring you any pleasure to screw people over either. And you wouldn't starve children to death for a mere few coins, after all. You may be a bastard but you're not a [censored] bastard.
Finally, regarding part 3, I don't think you can claim to be a good guy if you "go along with" the DB. It's a shame to miss content but they're so obviously evil that there's no joining them if you want to be "good". In fact, when you consider their line of work, it's really problematic for you to not deal with them right away. Every day you let them live is another day you're risking the lives of innocent people.
I played the airport scene in mw3 I think it was (I'm not a cod fan by the way and never will be). And when the terrorists started killing innocent people I didn't kill any of the people during that scene due to it seeming wrong. But I did choose to play that level and not skip it so that I got to see and play the full content of the game.
I haven't played MW3 and I doubt I will, so I have to say that I honestly don't know what goes on in the airport scene. If it involves shooting captured terrorists in the face to gain information about non-captured terrorists who are killing innocent people then count me in as a proponent. Torture is generally a bad thing, but it's worth a shot under certain circumstances. Those circumstances are rare, of course, but it could happen.