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.