I don't like to argument against other people's opinions. So I will just address this:
Good Karma and Bad Karma is your reputatiion. Roy is not known as a bad guy so people think killing him is unjustified even if you kill him knowing that he's planning on assaulting the Tower's residents...who are known to be assholes.
You are misunderstanding what karma is. Karma is not a reputation in Fallout 3, karma is a universal force about your actions, pre-planned depending on what the devs morality were when they made the game.
What you do affects the world, if you do "good" things, the world supposedly becomes a better place, you get good karma, but if you do "bad" things, the world becomes a worst place, you get negative karma.
If karma was a reputation, why would it change when you steal something or kill someone "good" when there is no one else around to see you do it? You can't get a reputation unless someone sees what you're doing.
Another proof of this is when you get out of Vault 101 and go straight to Megaton. When you meet Lucas Simms for the first time, he says that he doesn't know why, but he thinks you're alright (good karma) or that you have a weird look, the kind that means trouble, and that if you misbehave, he will kill you (negative karma). He says it's the feeling he gets from looking at you, it is not a reputation.
Tenpenny Tower comes across as a place that ought to have fallen apart within a couple of months due to the lack of food and water.
Also, Tenpenny Tower is the only settlement in the wasteland that has non-irradiated water through it's pipes. Not even Raven Rock has non-irradiated water.
Tenpenny Tower is a settlement that exists as a retreat for the richest Wastelanders. Tenpenny took the place, rebuilt it, and turned it into a fortress for those prosperous enough to live there. It's basically the closest thing to luxury in the setting. It's not a farming community but a place where people retire with their fortunes.
This causes some issues. They have as many heavy armored and armed guards as residents, and yet, Roy manages to kill them all by himself in the blink of an eye and without making a mess of the tower?