Well, in the comics they addressed this issue long ago by having things like "Damage Control Inc." which specializes in cleaning up after super battles.
It's important to also note that the whole "Reed Richards is useless" trope aside, technology invented by guys like him are also insturmental in this kind of thing. Basically if you have an entire universe of super beings out there, it presents solutions to a lot of the surrounding problems. In the movie-verse though there isn't enough supporting material to really explain it if in the next Marvel movies the city doesn't have parts of it still leveled.
Some super universes, especially those in RPGS (Gurps, or say White Wolf's old Aberrant setting) focus on civilly themed super-beings and even teams who do little more than public works and try and fill in the gaps between what other super beings do. Someone with say earth control powers, molecular control, magic, or similar things might be a great crime fighter or terrorist/villain, but not everyone is wired for that basically.
One interesting thing about the reconstructionist movement in comics is that it spells out in detail how problems coming from deconstruction such as "OMG the property damage" are generally solved by the concepts themselves.
(EDIT: Ooops, someone mentioned Damage Control already)