Honestly, when it comes down to it, this was the best option for Lelouch. These children had been toyed with their whole lives, they essentially would have been Rolo's, no family, no love, just born to be killers, and unfortunately there just isn't a future for children like that. Although he was originally going to just "Use" the Cult, I'm not so sure that it would have worked out all that well, V.V. isn't exactly a push-over, and I feel as if C.C. would have been in danger had he gone through with that plan. While Shirley's death definately propelled him, his actions weren't exactly monstrous, it's not like this was some innocent village, this was a place where weapons were being made from humans, better left destroyed.