While Civil War is a solid move and one I actually like a bit more as I think about it, I think it’s important to remember that applying real world logic to superhero stories is tricky at best and silly at worst.
For one thing, in a world of superhumans, supervillains are bound to arise. When that happens, you need superheroes. They are not optional. They are a necessary bulwark against powerful individuals who can destroy worlds by blinking.
I love The Incredibles, but it gets around the “What happened to the supervillains?” question by simply not asking it. And there are supervillains in this world, as implied by Frozone and Mr. Incredible’s conversations and by the appearance of the Underminer at the end of the film. I don’t mind that the focus of the movie isn’t “What happens when supervillains are allowed to run unchecked?”, and I’m glad it doesn’t bother trying to answer the question. But for the idea of banning superheroes to work you have to imagine all the supervillains going away as well.
Even stories that deconstruct the superhero ideal usually do it by either A) having a world with relatively few superhumans and B) having a character go mad and eventually be stopped by another superhuman. Alan Moore’s Miracleman is indeed a horrific glimpse of a world with an incredibly powerful mass murderer. His rampage only ends when he’s killed by another superhuman. Dark? Yes. Anti-superhero? Sort of.
Civil War’s “damning” evidence of the danger of superheroes is all examples of heroes stepping up to prevent greater disasters. Nobody wants the Hulk running around unfettered, but when a giant space dragon attacks the city, you are ultimately glad he’s around. Even the opening action sequence of Civil War is about how Cap and his team prevent bad guys from escaping with a bioweapon and, in the process, eleven people are killed and others injured. That’s bad, but when you consider the number of people endangered by the bioweapon and the possible death toll of that explosion, you can see that the casualties are very low.
Which doesn’t mean our heroes shouldn’t be criticized. Cap doesn’t ever justify the loss of life and damage by pointing out the greater good. But in this fictional universe, it is irrefutable that our heroes (yes, even the Hulk) have proven to be an invaluable asset to the Earth.
Real life is a hell of a lot more complex. It’s interesting to explore these ideas in a fictional universe, but it doesn’t mean that the real world parallels are going to pan out. In a world where a man flies around in power armor and a supersoldier fights evil with the powers of a red, white, and blue shield, let’s not get too carried away about the needs of “reality”.