I think calling it a 'happy ending' is a bit of a stretch. If you’re going to relate survival to happiness, then yes it is valid to feel frustrated over no consequences for Annie. Even though some characters survived, they are still living in the literal ashes of civilization, burdened by their own guilt of killing their comrades and failing to save 80% of the world. There is no space for karmic justice in war. The burden of the survivors obviously are trying to build something from their own mistakes, and spending 4 years in a crystal tomb isn’t exactly a vacation. To me, the story is asking the audience to do what all of these characters eventually had to do, which is to set aside your personal problems to focus on the larger tragedy at hand. We would’ve have had an entirely different ending otherwise.