If he walked near a window with his weapon and a sniper put a .308 in his head would you feel any differently? That certainly would have been justified as he had shown himself to be a direct threat to the officers on the scene.
Actually... without any hostages present, he was not a threat to anyone who did not willingly engage him. The on scene officers have the option to take cover, and wait. There was no hurry.
Me thinks the FBI HRT would be sitting there eating sandwiches right now and playing music (Unless they happened to bring Lon Horiuchi along)