Because the OP manga is smarter than just painting every-thing black and white, it's a big grey zone.
The Marines default mode is to be the good guys, the pirates are the menace to ordinary people.
How-ever, with such a large organisation as WG, where it seems to be the safes way to get a power grasp, of course some of the branches gets corrupted.
That has little to do with the major ideal of marines though, and more to do with the individual power hungry person whom comes and screw every-thing up.
Like Spandamn and those (Any-one remembers Spandamn, no there was an irredeamable bastard!)
The WG is not just one big thinking mechanism, it's a large group of people, many many individuals, trying to some-how work together.
Though their morals and principles as single persons often ends up becoming different.
Akoji is a person whom has exsperiences this big gray zone, and what the marines are cappable off, he has great sympathy for those simply cauhgt up in the middle of these circumstances and empathises with them.
That is what makes him different from Akainu is much more ruthless and straight-forward seeing the world as either there justice or no justice, he is way more black and white like that, with that much less sympathy.
Coby is a bright young man, whom truly believes in justice and the good the marines can do, for the good of people, he wants to be a hero and wants to help.
That is his motivation, not as a marine, but just as a person and a character.
Though.. there is one core thing that does make the WG.. kind of bad, and is a core problem, I think people have forgotten to bring up.
.. The WG are owned by the Celestrial Dragons! Those are the ones calling the shots on every-thing and dude.. talking about Douchbags!
No wonder with such stupid incompetent people as Celestrial Dragons pulling the strings, the WG is so fragmented.
But nope, this is not just such a simple manga as being. "Good vs. Evil."
It's people vs. People, whom each come from each their side and have each their reasons.. well usually.. we also have our just oure evil single villains..
But overarching, over arching, the manga is smarter than that.