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Koby had always believed the Marines were just. They brought with them the justice needed to deal with Pirates. At the time, his only altercation with pirates had been Alvida and she made his life a living hell.
And then he met Luffy.
Luffy, who was also a pirate but who didn't go out of his way to harm others. Except when they harmed him, or those he saw as his own. Additionally, despite being a Pirate, the thing Luffy was looking for the most was being free.
Being confronted with Morgan, and Helmeppo to a lesser degree, and the terrified gaze of the people they had been supposed to protect also played a part. Zoro scared him, but hearing that the man got tied up because he protected Rika from Helmeppo's pet wolf and killed the beast didn't make it look like the Marines were doing a good job at protecting the people.
He still wanted to be a marine though, even if it was to find his own justice.
Garp helped with that. The Vice-Admiral picked him and Helmeppo up from Shell's Town, and he had truly believed he had found his calling. Garp was everything he expected a Marine to be. He protected civilians and had a very set moral and honor code. He went his own way, and because of his reputation no one stopped him from doing so.
Finding out that Garp and Luffy were related shouldn't surprise him that much. Both of them were chaotic souls in their own way. Living at their own moral compass and letting that dictate what it is they wanted to do. So, when grandfather and grandson meet at Water 7, Koby isn't surprised to know that Garp has no intention of bringing Luffy in.
Things change again at Marineford, as he sees the brutality the Marines are capable of. Waging war against an emperor because one of his chosen sons bore the blood of Gol D. Roger. He didn't know Fire Fist, but the way the man looked defeated at having brought his father-figure and crew here cemented him in Koby's mind as being very family orientated. Something only added to when Luffy came falling out of the sky proclaiming them brothers. More chaos followed, and while he didn't know what happened, all he did know was that Fire Fist fell defending Luffy.
He felt it was his own justice to call for a ceasefire. To stop killing so many people.
Akainu disagreed, but the man's Ultimate Justice would get them all killed at one point. Being saved by a Pirate hadn't been expected either, but Koby couldn't help but admire Redhaired Shanks for what he did at Marineford.
"The fact that I have met a lot more Pirates that are willing to go the extra mile for their loved ones compared to Marines, also says a lot," He couldn't help but whisper in the privacy of the barracks. Shaking his head, he looks up out of his window, "Because really, what is Justice if people are taking it as away to do whatever they want, kill whoever they want and believe that because they believe it to be true, that's all there is to it?"