If the NSA tried to stop the process and acted against the orders of the Commander-in-chief, Obama should then recall the US Military and destroy the NSA with brute force, treating it as a hostile domestic militia that is attempting a coup. Game over. Sound far fetched? No, it's just a standard issue government revolution, no different than what has gone on throughout history all across the map.
The Obama administration has decided to preserve a controversial arrangement under which a single military official is permitted to direct both the National Security Agency and the military’s cyberwarfare command despite an external review panel’s recommendation against doing so, according to U.S. officials.
http://www.washingtonpost.com/world/national-security/white-...