I'd have to imagine that conspiring with one leader to assassinate another leader would probably be frowned upon by Starfleet. What was the mission to begin with? Simple exploration? Did these people know about starfaring civilizations prior to your gang showing up on the scene? Did the Captain violate the Prime Directive to begin with by not taking proper precautions to cover their identities?
Definitely going to be trouble for the officer. But I imagine that intent and the ramifications of the violation will play heavily in the punishment.