I have nothing to add except that I had a similar experience. When I returned to the tower to find it deserted and the gate wide open, I was filled with disgust and anger.

I went right up stairs and murdered Roy and his two-faced, helmet headed goon, bad karma be damned. I left his girlfriend wandering aimlessly by the elevator.

I guess I can only compliment the game for arousing a genuine sense of total resentment in me. I wanted to kill Roy. How often do we really want to kill the bad guy?