Why not make a character who believes what he/she is doing in the Dark Brotherhood IS good? After all, someone had to request that person be murdered, so you're simply acting in the name of society. People are forced to live under the law and morality of the Empire, or else go into the wilderness and get eaten or mauled by animals. So your character could merely be giving the power to the people and acting on their wishes, without making any real moral call either way. Much like a guard of the Imperial Legion.
Plus, not everyone you kill in the Dark Brotherhood is completely innocent.
Spoiler Rufio, I'm looking at you. :stare:
Or, you could always play as a Morag Tong sympathizer or something along those lines, killing people honorable instead of from the darkness when they don't expect you. That'll cost you all of the bonuses though.