The subversion of tropes goes back all the way to the original Mobile Suit Gundam, though a little more subtle due to the studio wanting to make a show to sell toys and the director wanting to make something with a actual message. It has: -a 'good army' that could easily be the 'bad army' in a more optimistic show -the protagonists dealing with callus military leadership -sympathetic enemy soldiers dealing with their own incompetent and callus leadership -the war taking a huge psychological toll on the protagonist and all of them end up worse off for having been a part of it

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.