It doesn't damage anything. It only shows that the only person who has no real clue about CLU is Sam. To Sam, CLU was just another program, something that could be shutdown and deleted from the outside. He didn't know how his father created him, only that he created him. For all Sam knew, CLU could have been programmed in the same manner as any other program circa 1989. If you feel it damages any characters motivations and intelligences, could you please point out examples of what you mean?