Just the fact that they did something does not mean that they still have control over it.
Especially after the Prism scandal.
Hiding something like this is simply not possible in after-Prism paranoia world.
and don't forget that the NSA relies on it's operatives going into harms way into foreign and hostile areas.
you now have to imagine a scenario where they lie to them, and have the operatives allow themselves to be lied to, and say all their communications will continue to be safe and secure so continue doing what you're doing? either way, the NSA has suffered irreparable damage as a result of these so called revelations.
i prefer the simplest explanation and that is to continue to believe that the Internet is ripping open age-old secrets and increasing the dissemination of the truth. to expect one US centric organization to be able to buck that trend over the long term is not viable, imo.