Oh really. Got proof of that? Are they abandoning the Sears Tower or the Transamerica Building?
That's one shaky premise.
I'll start by pointing out that (A) neither the Sears Tower nor the Transamerica Building have not been the targets of any terrorist attacks yet while the WTC was the target of two attacks designed to destroy it, one of which succeeded and (B) both of your examples probably benfit from long term leases that companies are reluctant to break.
That said, the Sears Tower has not been without occupancy and valuation problems since 9/11 (see http://www.suntimes.com/special_sections/sept11/illinois/searstower.html and http://www.conway.com/ssinsider/pwatch/pw021111.htm, for example). A more relevant example, the Empire State Building, has lost tenants but not terribly so (http://homes.wsj.com/columnists_com/bricks/20020912-bricks.html). It is, however, a very solid building that would be harder to hit, due to surrounding buildings like "the EIB Building" and the Chrysler Building nearby).
That said, it doesn't really matter what you are I think. What matters is what the owners think, since they are the ones gambling their income on the choice. They seem to believe that it will be unnecessarily difficult to find tenants for a really tall building. There is also the issue of insurance which will be, no doubt, higher for a tall landmark building that is likely to be a terrorist target. I think the latice work structure addresses that concern while giving NYC something tall and appropriate for its skyline.