Occam's Razor suggests that the simplest explanation is usually the right one.
The former head of the TSA has said publicly that when he became head of the TSA he wanted to end a lot of the post-9/11 security crap (liquid bans, shoe removal etc). But when he took up the position, he was shown examples of actual threats that those security measures were stopping (or could stop) and that removing them would increase the risks.
My guess is that Obama when he took up office was shown examples by the intelligence people of things that had been detected or identified thanks to the wholesale spying (and remember we aren't just talking about terrorists, we know from the leaks that the wholesale spying is being used to catch drug dealers and organized crime figures too) and as such realized that shutting it down WOULD make the world less safe.