I haven't seen the clip in spiderman so I can't comment. And I don't recall that simpsons episode either. But I doubt people will be offended by that, just cause of this horrific incident. All of these started before the incident, therefore not knowing about it, therefore not 'cracking' at it or implying anything about it. So it isn't disrespectful to it at all. Do the so called towers resemble the WTC towers, ARE THEY the WTC towers? That may make a difference.
In any case, if they remove stuff, good for them... It's no big deal. You shouldn't care that they DID remove it, and if they don't... You probably shouldn't take offense to it, but it's understandable if some people do.
-RSI