I mean, I think that's a valid reading. And if in our world the Japanese military had been ordered by the emperor to do the Rape of Nanking and afterwords overthrew the government as a reaction against that, it would definitely read like that. But though it definitely isn't as critical as it should have been, it's still a far cry from all of the actual WWII military apologia you can find in anime. There are a whole lot of writers out there who are open about thinking Japan has never done anything wrong, and I really don't think she's even close to being that. Though like I said, it's definitely way more sympathetic to the soldiers than I think is fair. (Also, the author has said that she views the series as being more about the genocide carried out by Japan against the Ainu people indigenous to Hokkaido.)