Charles saw in lelouch the same things he saw in himself and he was proud, proud of his sons dedication and ability to raise a rebellion (likely the only one in recent history) even if he was mad at him for it. Asking this question is like asking why didn't lelouch just shoot shirley after the mao disaster?. Charles did his memory rewriting shenanigans since Rolo was replaced for Nunnally. The bomb that Nina made towards the end of season 1 was a dud and didn't go off. Lelouch geassed Shirley to forget Lelouch entirely meaning she wouldn't remember that he was Zero or any other past memories with him.
When Shamna's Geass activates, Shamna is sending her own memories back 6 hours in time, and using these 6 hours to prepare for whatever Lelouch has in store, and she's sending her memories back every time Lelouch successfully interferes with her work. The main characters then play out the timeline and unknowingly go through the same sequence of events each time that Shamna's Geass activates.. Lelouch's back is turned toward us as he faces the crowd. For a brief moment, I thought Lelouch did as his mother had and projected his consciousness into the mind of an unsuspecting child. Or any spectator, really. Then during the sequence where Nunnally telepathically realizes Lelouch wasn't really evil, we see his life flash before his eyes.