The simple fact of the matter is that art imitates life, and despite what some may say or believe, it's rarely the other way around. There are all different kinds of tragedies that affect human beings on a personal level, whether it be terminal illness, drug use, terrorism, or murder. On one of my best friends, a beautiful 21-year-old girl, was recently shot and killed accidentally by a police officer during a home invasion in which the officer fired 8 shots at the criminal who was using my friend as a human shield. One of those bullets hit my friend in the head.
This was one of the most personal tragedies I have ever faced, and it has been a tough summer because of it. However, isn't that a scenario you've seen in films maybe dozens of times? Maybe with different, less tragic outcomes, but similar nonetheless. Will I think of what happened when I see someone's head blown off in movies from now on? Maybe. Sometimes. But I'll never hold it against a film for having imagery that hits close to home for me. It's only natural. It's going to happen.
So, I do understand the compassion for what happened on 9/11, especially for those personally affected by that monstrous tragedy. But I think it's a little unfair to harp on it when it comes to certain film imagery or bring it up as a negative aspect of Man of Steel, especially since we're talking about super-powered beings punching each other across a city and alien spacecrafts leveling buildings. It wasn't an issue when watching Independence Day (since nothing like 9/11 had happened yet), and it shouldn't be in issue forever. When we frown upon this type of destruction in huge sci-fi epics like MOS and Star Trek ID, the terrorists have accomplished part of their goal, IMO. Fear and discomfort.