It doesn't seem unreasonable to me that the responding agency would want to have control of the scene. Worse than crazy flooding would be crazy flooding combined w a plane crash. The light aircraft that the article mentions likely would not see a drone and could easily hit it. Perhaps FEMA should be incorporating this type if drone into their response plan and I'm sure they could be doing it faster but having civilians flying unannounced and practically invisible as high as 1500 ft seems like an opportunity for disaster.
EDIT: From FEMA's own documentation http://www.fema.gov/pdf/emergency/nrf/nrf-esf-01.pdf: "DOT/Federal Aviation Administration (FAA) is responsible for the operation and regulation of the
U.S. National Airspace System, including during emergencies. "