And to your first point, the "good army" did become the "bad army" by the time of the sequel, Zeta Gundam. Once they're no longer on the back footing, the "good army" becomes a ruthless occupying force, operating almost entirely without oversight and under the direction of officers who are all too willing to cover up war crimes. But it still makes sense because you can see over the course of the show how such shift could happen in the inter-war period between the One Year War and the Gryps Conflict.