Bleeding Cool spoke with David Goyer, who said the following:
One of the things we were hoping to depict is that Superman is not a god. We say he’s a god-like figure but he’s not omnipotent. Even in the comic books he cannot save everyone. I think people die [in Metropolis]. Clearly hundreds if not thousands of people have died while the gravity machines are going off. There were probably even people who died in Smallville.
When you’re dealing with a threat like this, there will be collateral damage. This is something that hadn’t been depicted in comic book films is what it would be like if these powerful figures did clash, if The Hulk and Thor fought, people would probably die. Particularly in this case where Zod and the Kryptonians really don’t care if people die. I think people died and I’m sure that upsets some people.
We knew that people would be upset by some of the choices we make. We got some grief when we did Batman Begins. Now people think what we did was great but when Batman Begins first came out, people were upset by some of the choices we made.