There was discussion of this a while back. Sir Ian McKellan mentioned it on his website as well. My understanding is that Perter Jackson, et al. are taking the following stance:
1) The World Trade Centers Twin Towers weren't even built when LOTR was written & the 2nd book was named. (iirc)
2) The book is called the TWO towers, not TWIN Towers
3) Renaming it would draw more attention to the title, and thus remind people of the tragedy, rather than deflecting attention.
4) It would be disrepectful to the author moreso than disrespectful to those who were killed in the terrorist attacks. Since how the name is disrespectful isn't really clear in the first place.
Anyway, that's what the folks who made the movie said back around February or so.