Intelligence agencies are full of smart people. They know that secrets this big can't be kept indefinitely. Once the cat's out of the bag, then the panopticon comes into effect. They have factored in the effect on free speech into their decisions.

And it's not even that bad in principle. In a more perfect world you want to have is freedom of speech and an organization like S.H.I.E.L.D. which secretly scoops all communication to protect the public from greater threats. Unfortunately, what we got instead is a kind of Hydra that lacks ambition for world domination.