Er what? I killed him and I did not get any light side or dark side points. My SI enjoyed it though since she said "killing you will be such fun!" then shocked him into oblivion and told they two cult members to be my mouth piece.
I know there is a way to kill him without gettting any light or dark points I know since I leveled two dark side SI to 50.
If you use the "killing you will be such fun!" option you won't get any alignment points however if you don't take that opportunity and continue the conversation it ends with the choice of sparing him to lead your cult for dark side points or killing him for light side points.