Guess the Sword organization was Oda's way to introduce the new marine group that will take over after Akainu's regime in the marines will be dismantled, which explains why they are allowed to go rogue, and do things without their permission and with Coby's dream of becoming a marine admiral, and his recent hype as the future of the marines, he'd ultimately end up being the leader of that regime, which funnily enough would completely antagonize Akainu's
thorough justice just like in MF
With the little Coby ultimately turning the marines into a new leaf