Yeah, I think the key to any deconstruction is the idea that the subject being deconstructed is itself the problem, with the main antagonist being “human nature” rather than any external evil. In Watchmen, for example, all of the problems arise because some retards put on spandex and beat each other up in the streets, thinking it would help clean up crime. Capes aren’t doing anything good for society, they only exacerbate existing issues and make them even worse, to the point that the head honcho cape eventually decides to destroy NYC with a giant squid monster so that he can convince everyone to keep supporting the superhero grift.
In both Madoka and Evangelion though, the root source of conflict is purely external, and the subject of interest is established in-universe to not just be the best solution, but in fact the only solution. Magical girls are the only things that can defeat witches, much like how Evas are the only things that can defeat angels (…for the exact same reason, now that I think about it), and the witches/angels themselves are a threat put upon by humanity by greater forces well beyond our understanding or control. It’s impossible to do a “magical girls/giant robots bad” deconstruction when it is explicitly established in-universe that magical girls/giant robots are the only way to deal with the threat at hand.
Another good example of deconstruction vs. subversion is Starship Troopers vs. WH40K. In Starship Troopers, the bugs themselves aren’t actually the threat, just the pretense for fascist hypermilitarism. In 40K on the other hand, despite how awful the Imperium is, they’re still the lesser evil compared to Chaos and the Tyranids.