On this issue, I like the way you think on missile defense.
Just the idea of potentially losing minutes on a confirmed inbound missile which could potentially be carrying a nuclear paylod is unsettling.
Leave it to bureaucrats to waste time on this 9-11 call and play the blame game later. The rules need to be set up in advance, but definitely let the military handle this call.
BMD (and to a lesser degree, even regular air defense) is a game of "shoot first, ask stupid questions later and sort it out when its on the ground". Anything that slows the time from launch detection and positive identification to weapons-free and engaging the missile is unnecessary and needs to be eliminated.
When dealing with weapons that can kill millions if they detonate, you don't ask questions, you just open fire until you're absolutely certain that the target is destroyed. Then you shoot it a few more times just in case.