Your right. We can't nuke. The Japanese surrendered because they wanted the bombings to stop. They valued their homeland. The terrorists don't give a rats.
So, basically, we will be stuck with the fact that these kinds of attacks will be a way of life.
The end game will be a re-distribution of societies industry and population across the country side. Who will want to live in urban areas after the first bomb goes off? The more desireable rural locations will go up in value and our cities rot.
As a practical matter, that appears to be the case.
It is a war, though, but a new kind of war. This one won't be won until the children of the terrorists view their parents as tilting at windmills. Or something like that. A generation could see the end of it, but the active phase could go on like the IRA, on and on at a low level until the children just don't see the point anymore.