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.
For sure there will be a debate. I did some work a while ago at a regional IRS center, my first impression was; why is this center spread out so far and wide, acres and acres of a one story building? They simply answered, security. This is nothing new.
BTW, the "War on Terrorism" sounds too much like the "War on Drugs." Sounds fishy.
The last really biggy was Saddam's front line; which we easily attacked from behind.