I'm looking for a manga where the protagonist was fighting for justice, until they find out that things will just never change, and then join the other side.

Example:
Megalomania - A war against humans and Ajins (life-forms created by humans for labor), the main character is a hybrid of both so she dealt with as an ajin. But she still fights for peace of both races. And (hopefully) she joins the side of ajins.

Well, I'm not 100% sure but Scryed might fit. It's not like the protagonist is initially fighting for the 'good side'; more like he doesn't give a damn which side he fights for, and doesn't even want to take sides anyway. Still, I get the feeling you might like it.