First of all trying to find a logic or scientific explanation to religion is not always good. Science ifis a progressive information. New evidences can prove old theory or rule may not be correct.Still, If you need a reasonable explanation to stoning of Satan, this may help:
cognitive dissonance: changing attitudes to justify behavior
"The theory of cognitive dissonance states that when people become aware that their freely chosen actions violate important or relevant attitudes, the inconsistency produces an uncomfortable state of arousal called dissonance, which motivates people to change their initial attitudes to make them consistent with their behavior. For cognitive dissonance to occur, it is important that the attitude is important and self-relevant."
In psychology, actions affect attitudes or beliefs. So stoning satan is an action. Even there maybe no satan there. But you symbolically stone him. At this point your brain work like this: "I stoned satan, I can stone only bad things, So Satan is bad, and after stoning him, how can I do what Satan ask me to do."
At this point your action change your belief and you don't do sin as much as you did before.
Stoning satan one of the important parts of Hajj. You can find any resources easily to explain it in Islamic perspective.
And you can also find some resources that claim stoning satan is wrong