It's not really a choice, because in the end you get more powerful by not harvesting the Little Sisters. The only reason to do it is to see the evil ending cut scene.
I'm amused by the joke, but I don't consider it a spoiler to explain how one bad act ever leads to the uber-evil ending that has no connection to the rest of the game. It's just pointing out that the claimed 'moral choices with consequences' feature is a farce.