Lack of understanding of the rabbi’s words

The rabbi said in a class on conservatism and tradition that a Jew who kills a person even though he knows he is not worthy is only because of theoretical rules: “The Jew must be killed, and that is how it is interpreted.” How does the rabbi explain the story of Shimon Ben Shetach’s son who was framed {like Rapool, like Yaakov Ne’eman, “I heard Ben Yair say in my ears that I am going to stab the fascist,” testified Shebs. Kahalani, etc., etc.}
In the Midrash of the Ten Commandments (Otzar Midrashim Eisenstein, page 461):
As it is said, R. Ben Shetach hanged eighty women witches in Ashkelon. When he did so, relatives of the witches came and appointed a day and hour and testified that R. Ben Shetach’s son had committed an offense that required stoning, and they ordered R. his father to be stoned even though he knew that he had never sinned. Since they appointed their testimony, they brought him out to be stoned. R. Ben Shetach’s son said to them, “If I committed this offense, the witnesses and all Israel will be clean and my death will atone for me. If not, all my sins will be forgiven me and the collar will be hung around the neck of the witnesses and all Israel will be clean.” The witnesses said, “How can we shed innocent blood?” They told him that they had testified falsely that their father had killed our relatives. R. said, “It is already written in the Torah that if he does not testify and bears his sin, since he has testified, he will not return and testify again, and they will kill him, and a collar will be hung around the neck of the witnesses.” And for this reason, a person should guard himself from slander and guard himself from the troubles of his soul.
Thank you very much, Rabbi.