Tom Logan wasn't a killer by nature. When the gang hung Pete Marker as revenge for Sandy being hung, they did it without Tom. In fact Cal told them: "nothing to Tom now." because he knew Tom would disapprove. So although Tom was angry about Little Tod's killing by Clayton, and had the drop on him when he was in the bubble bath, he couldn't bring himself to murder him in cold blood. Tom was a low life thief but not a murderer. He finally kills Clayton after he's been driven to near madness by losing the only real family he had. His entire gang. Plus he knew as long as Clayton was alive he was a sitting duck, so killing him was a form of self defense. It was also self defense when he killed Braxton. There are degrees in criminal behavior like everything else in life.