Our Gemara on Amud Beis discusses why the Gazlan (brazen robber) only pays the principal, while a Ganav (stealthy burglar) pays double as a fine. The Gazlan simply does not care about anything or is motivated by some drive that is beyond any shame. However, the Ganav obviously feels some shame as he steals under cover. This man is more fearful of people than God, and therefore is punished more harshly. Rabban Gamliel adds a parable to explain this further: 

To what is this matter comparable? To two people who were living in the same city, and both of them prepared a feast. One of them invited the people of the city to his feast but he did not invite the king’s sons. And the other did not invite the people of the city and also did not invite the king’s sons. Which of them deserves a greater punishment? You must say that it is this one who invited the people of the city but did not invite the king’s sons. Likewise, both the Ganav and the Gazlan show disdain for God, but the Gazlan does not display more respect for people.

Ben Yehoyada asks how does Rabban Gamliel’s mashal add insight? Noticing the use of the term “King’s sons” in the parable he explains that Rabban Gamliel is addressing those who believe that God is too lofty to look down upon the world, and leaves it to His underlings, i.e. the forces of nature or spirits that idolaters worship. Even if someone had such an incorrect notion, acting as a Ganav is still disrespectful to God, because he is attempting to hide from God’s emissaries. This is what is meant by the King’s sons in the parable.

Ben Yehoyada’s explanation works for someone who has a distorted theology but at least holds himself accountable to some higher powers. What about the complete atheist who behaves as a Ganav? He is not hiding from Man more than God, he just doesn’t even believe in God. While parables that explain mitzvos do not have to work perfectly for every situation, I believe we can still understand how the parable might apply to the atheist Ganav. A sense of shame and morality is not necessarily dependent on belief in God, although certainly enhanced by it. Thus, the Ganav who shows some sense of shame, should also have been motivated by his shame to refrain from this action altogether. Therefore he is punished harshly. On the other hand, the Gazlan is obviously compelled by internal forces that show no regard for anything. Whatever his issue is, extra punishments will not have much effect. 

Hashem is merciful and does not punish if there is no value in it. This is something to think about when parents or teachers discipline children. Some children need the discipline and punishment to learn a lesson. However, other children may have challenges and internal pressures that will not be mitigated by harsh punishments. How can you tell what is appropriate? If the child behaves in a way that is so self destructive that the punishment seems to have no deterrent effect, In such a case, it probably is because the child is battling with forces that will not easily be subdued. The child certainly needs discipline of a sort, but not punishment. It is notable that the actual etymology of the word discipline is to teach or instruct, not punish. It is not good to throw punishments on someone who lacks the self control or cognition to manage his behavior even if there will be consequences.