It’s not novel at all - security researchers have been doing the same thing for literally decades. Worms often have kill switches built into them, that if the researchers can figure out allow them to stop it globally.
The question isn’t “is this possible and has anyone ever done it” - it was was “has the FBI ever used a botnet’s existing C&C patch all the infected hosts”?
It doesn’t seem like it, but I don’t track this stuff closely so I’m happy to be corrected.