You're talking about a policy of federal government that should be decided on the government level through Congressional legislation or even courts if they have jurisdiction in such matter (outside of FISA or something similar).
This issue should not be played with via a bogus lawsuit against private company with public oversight that has simply been a conduit of the policy.
If these groups think that such a program shouldn't exist or should be limited in what it can do (which is a moot point now), they can advocate this to Congress just like they are invited to do on many other issues. Their lawsuit against AT&T exposes their true intentions, which are to harm an administration which committed no specific violations of the legal program.
It's like Fitzgerald proceeding with "investigation" after the WH while he knew from the start that a) no crime has been committed, and b) who was the one who "didn't commit" the "no-crime".