I'm sure someone will note these and many other factors.
How will they rebuild these towers?
Getting away from engineering, the concept in the cultural sense, of the great tower as a symbol of 20th century business might be coming to an end. Or, at least until technology will allow towers as these to be built in a manner that allows safe evacuation, even in extreme cases as these.
Albeit a rare case, but one that has just set precedent that will be followed by future terrorists. Big jet liners can fly accross oceans. All the internal security cannot assure anything. (with less fuel to be sure)
Maybe these towers are done for, in the same way castles were done for when gunpowder and cannons came about.
You have essentially answered yourself. Fort building went on long after cannons first started breaching stone walls. The last really biggy I suppose was the Maginot line, not counting all the nuke shelters.
The ground in Manhattan's financial district I suspect is just too damned valuable to leave as open space. I can't imagine New Yorkers accepting a smaller building, it would be admitting defeat. Neither can I see them settling for anything but the tallest building in the world, and the ground site should be big enough. If not, they will make it bigger.
As for the plan business, that was easily preventable, and we should be kicking ourselves in the butt for not expecting someone to try something already put into the movies. The government solution will cause real headaches, but he headaches will soon force the arrival of real and intelligent solutions.
Overall, the thing least likely to survive this event will probably be the Bush administration. Over 60% of Americans say we are at war. Over 60% say they don't know who we are at war with. It's a near impossible plate for anyone to digest.