I think that is unlikely as it isn't as though Koby is the sole Marine with good intentions.
Well, even Akainu likely has good intentions, he is just willing to kill entire islands or his own troops for minor transgressions in order to stop every single last pirate in the world and prevent the fall of the government that serves as the only barrier to everyone being victimized by criminals.
But Koby isn't the only Marine who is also not willing to become as bad as what he is fighting to achieve those good intentions. In fact, most of the Marines seem to be generally good people who genuinely aim to serve and protect others. Even the Revolutionary Army's commanders don't think of the Marines as the real enemy and don't go out of their way to attack them.
Unfortunately there is some messed up stuff, primarily coming from the Celestial Dragons, that the Marines have to accept as "for the greater good"– stuff they can't really do much about right now, but ultimately the amount of good they can do tips the balance in favor of continuing to serve. Then again, the majority of the Marines probably don't even know about the slavery or underground weapons trade or child trafficking that the organization, or those related to it, engage in. All they know is that if they don't get out there and stop the pirates, every village and island across the world is going to be ruled over by some petty despot who got just enough power to abuse the town.
So Koby swinging from Marine to Pirate, especially after being kept a slave by pirates for two years and only been given the opportunity to become what he has within the Marines, it would seem very odd for him to decide to abandon everything and become the thing he hates most. In fact, when it comes to Luffy he likely makes the justification that while Luffy and crew call themselves pirates, they don't engage in any actual piracy and instead and pretty much doing what the Marines would do if they didn't have to answer to the World Government.
It is likely the Marine organization will survive to the end of the story, they just won't be answering to the Celestial Dragons anymore, and Koby will be a major player in it. And they will still be the main force out there fighting the pirates that are actually stealing from and murdering people across the world.