To the modern mind, penalties of this sort seem primitive and savage. The person who violates the Shabbat harms no one. Why does he deserve to die?

Rav Noson Weisz explains that death penalties for religious offences are consequences rather than punishments. He explains that the capital penalty designated for Shabbat violation is there to inform us that for a Jew, the act of desecrating the Shabbath corresponds to jumping into a river without knowing how to swim.

Let us imagine the skeptic who does not believe that anyone can die by drowning confidently jumping into a river and drowning as a consequence. Would we consider his death by drowning unjust or unreasonable because it is contrary to his sincere belief that he would not drown? Of course not! In the same way, if a person actually inflicts a fatal spiritual injury on himself by desecrating the Shabbat, he will surely die regardless of his belief in the validity of the Shabbat laws.

Just as there are many activities that injure (sometimes fatally) the body, so too there are many activities that injure (sometimes fatally) th soul. The capital offences of the Torah are there to warn us of the potentially fatal spiritual activities (and thus help us avoid them).

As Rav Weisz explains: 'According to the Torah, our souls are who we essentially are; our bodies are merely the space suits we wear so that we can function in this physical world. It follows directly that when our souls suffer a fatal injury there is no need to keep wearing the garment whose sole function is to enable the soul to walk around this physical world'

Indeed the purpose of Mitzvot Lo-Ta'aseh (the 365 Negative commandments)is to prevent us from causing an injury to our soul, and the purpose of the Mitzvot Aseh (the 248 positve commandments) is to refine one's character / perfect one's soul, (See Rabbeinu Yona in Shaarei Teshuva, Shaar 3 or 4). The overall goal of 1)not-damaging our soul (by keeping the negative commandments) and 2) perfecting our soul (by keeping the positive commandments) - is to 'metaken alom bmalchut shakai' 'to fix the world in accordance with the kingship of Hashem'.