I understand what you're saying, I don't think that's a good idea, and there's a reason that you don't see that done in the comics anymore. The problem with that is that you're not Superman anymore, if any thug on the street can hurt you with a gun, laser or otherwise. Part of the selling point of Superman is that he's powerful, and so trying to find an obscure weakness for him so you can do the typical 'field of thugs' type of level design might make sense to fanboys, and even normal fans after sufficient explanation, but it's not going to feel like Superman. Especially if you allow people to be Superman in other ways, such as being able to dive bomb and plow through normal thugs.
So, your idea makes sense, but I don't think it works out to fun gameplay, or gives people what they want from Superman, which is feeling very powerful.
The issue with a Superman game is figuring out how to hurt him or lose a life aside from kryptonite. He can be killed and hurt obviously, but the only thing that can aside from the aforementioned rock is other alien creatures on par with or above his strength level.
It sounds like we already know what hurts him, so that's what you base your game around. Instead of trying to make Superman into Batman, see what Superman does and find the gameplay that accentuates that. Superman has big drag out epic DBZ-esque battles... pull some QTE stuff ala the DBZ games and Asura's Wrath and some Shadow of the Colossus world design and line up 10-20 of Superman's bruiser villains, and lets be Superman. Throw in some environmental destruction and we have a real party!
If it were me, I'd pepper the landscape with Easter Eggs, and people that need to be saved via completing puzzles (aformentioned problems on different sides of town, bombs that need to detonate somewhere safe, environmental disaster rescues, etc) and you can have an actual game on your hands.
I don't see why this should be an issue inherent in the character when translating him to a good video game when it clearly isn't for the comic writers. They understand that Superman's trials aren't about hurting him. They're about impossible feats. Bomsb on opposite ends often city. A shuttle crashing at the same time as a hostage situation at a bank is getting out of hand. This is the challenge of being Superman. Not "getting hurt." leave out the garbage about finding a way of hurting him, or having metropolis have a health bar. No healh needed (except maybe rarely when affected by Kptonite, but this could be similar to the scarecrow sections in terms of difficulty to control and whatnot). Make the feats the challenge.
That sounds like a health bar for the city. When someone else gets hurt, you lose the game.