Unfortunately, they always manage to find a way to give orders from prisons, even from maximum-security prisons and since they are already there, there is no way to punish them. The only way is to execute them, but the law enforcement doesn't do that because, as far as I know, to sentence them to death it is necessary to bring them out of solitary confinement for trial for a certain period of time and they can use this period as a better possibility to give orders to their organization outside. I remember watching a documentary about a boss of the Mexican Mafia who wasn't prosecuted for this very reason even though his people outside were convicted.
I am not a supporter of the death penalty, but if we speak theoretically, that would be the only way to stop a mob boss from running the organization.
I remember about Mariano Agate, an Italian mafioso who stays in a 41 bis prison which is so strict that it's considered "torture" by some people outside Italy, and he managed to create an organization with ties to the Colombian cartels even from there.