You have to remember, the default answer to "Can I sue the government?" is No. The only suits you're allowed to take to trial are ones the government has allowed themselves to be sued for.
For example: https://en.wikipedia.org/wiki/Federal_Tort_Claims_Act
While I think the entire idea of sovereign immunity is bullshit, the chance of the doctrine being overturned is next to 0. So we have to live with it. The point is, you're kind of lucky to even get as far as getting this dismissed over state secrets.
The real problem with the state secret doctrine is when the feds intervene in a suit between two private parties.
AFAICT, this was not a torts lawsuit. Wikimedia was not suing for damages, it asked the courts to declare certain government practices illegal and/or force the government to desist these practices.
This is the meat of the problem with pervasive surveillance. Until this matter is resolved in such a way that makes any surveillance without a warrant be deemed unconsitutional, the idea of 'freedom' is only a ghost in the U.S.
These kinds of abuses must be addressed by Congress, not the courts.
The programs in question here are also clearly not national security matters. They were made public, are illegal, and the security of the nation was not affected in any way.
The whole house is built on a foundation of lies.