If Obama wanted to fundamentally alter this problem forever, he'd go on national TV and tell the American public exactly the situation - that the NSA is so powerful he can no longer control it. Then he'd convene with Congress, and order the NSA to be dismantled immediately (and rebuilt under a different, much more restrained spec).
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.
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.