Actually, they did raise a very valid point in defense of what happened. Sure, taking out the planes before they hit the WTC would have prevented tremendous damage and death, but that wasn't physically possible.
Taking out the plane that hit the Pentagon, though, would have been different. The area around the Pentagon is home to many office buildings, apartment complexes, houses, and a huge shopping mall. In what was perhaps the only lucky thing that happened on September 11, the guy flew the plane into the part of the Pentagon that had been hardened during a renovation. That definitely saved lives.
Now, if that plane had been shot down in the area around the Pentagon, the debris, burning fuel, and so on would have been spread all over a densely populated area. Would the casualties been higher?
We don't know.