Does the Torah condemn and punish or not?

Hello Rabbi ,
 
In the harsh coronavirus column, the rabbi laughed at the Torah’s perception of Magna and Mitzla.
 
On the other hand, in a conversation with Dr. Roy Yuzovitz, the rabbi does say that when you want medicine, you don’t study Torah but go to a doctor, but the rabbi also says that he believes that it does have a positive effect, probably in metaphysical ways (50:30 from the opening).
 
I understood the rabbi’s view to mean that in this world there is physics, and there is free will that is included within the framework of this world, but it is above physics, meaning it is not dependent on its chain of circumstances.
 
I didn’t know that the rabbi had an opinion and belief that even commandments like Talmud Torah have an impact and change reality in practice without being dependent on physics (like free will). I would appreciate it if the rabbi could elaborate on the subject.
 
Best regards, Ehud