There are two fundamental questions in regards to the בן סורר ומורה.
The first is, Don't we believe that every Jew has a chance to do Teshuva, and deep inside has the potential to climb out of whatever pit he has dug for himself? How can we kill a young man על שם סופו - because of what he will be in the end? Isn't there free will? How do we know for sure that he will end up so bad?
The second question is, What does the gemara mean when it says that the case of the בן סורר ומורה never happened, so it is there to learn and receive reward?
I believe that these two questions actually answer each other. The very fact that the בן סורר ומורה case can never happen teaches us indeed as we originally assumed. There is never really a possibility of a child being so bad that there is no hope and he is killed because of where we see him going. The Torah gives us this whole involved case with all these prerequisites to show us that it is impossible for a person beyond hope to really exist. Then why does the Torah even mention this case at all? The answer is so that we can learn this very lesson from the Torah - דרוש וקבל שכר.
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