The torah allows a number of punishments including stoning for a variety of “crimes’ (putting aside whether or not we have a Sanhedrim)
To set the record straight, the Torah does not “allow” stoning. In certain cases the Torah *mandates* stoning for the violation of certain cardinal laws with eidim, hasrah, and the Sanhedrin. And conversely, if any of those criteria are not fulfilled, the Torah *prohibits* stoning.
In no case is stoning a reshus, left to one’s own preferences.