Well, the death penalty might actually be a mercy compared to a life imprisonment in a medieval dungeon. Prisons back then were not nearly as comfortable as they are today in most of the developed world. Imagine spending the rest of your life in a tiny, dark, cold and filthy cell slowly starving to death on a diet of rotten food. Which is what the MC suffered before their execution and which is the most realistic alternative.
A pre-industrial state with historical levels of crime simply could not afford to give common criminals better treatment, which is why harsh punishments were the global norm during the era (and still is in many poorer countries, for practical reasons if nothing else).
The idea of rehabilitation trough penance (or education) might also not be a thing in the setting, since it depends a lot on religious and philosophical schools of thoughts which may or may not exist.
Granted, in the case of the MC executing them might prove to be an extremely costly mistake if they return to destroy Leon and his kingdom. But if that happens it will be far too late to reform the penal code, and it’s hardly something to be expected from your average rapist or murderer.