I have the sollution if you want to kill Roy Phillips and his followers (Michael Masters & Bessie Lynn) without receiving bad karma.
Activate the quest by talking to Chief Gustavo and go to Roy Phillips, through the Warrington Trainyard.
Watch out for Feral Ghoul Reavers, they have more HP then the glowing ones. Talk to Roy Phillips and tell him, that Gustavo wants him dead. After that, tell him that you will spare him for some caps.
He will get hostile so you can kill him without receiving bad karma.
After that kill Bessie Lynn (after she gets hostile, sometimes she doesn't and you have to start over). On the way back you wil meet a hostile Michael Masters, kill him and get back to Chief Gustavo.
He will give you 500 (or 700 caps) and you get the achievement.