The government must have consented to the presence of the plaintiff's attorney, or they were asleep at the wheel. IMHO, of course.
Yes -- I was the government and I consented. 
Correct. But we hardly ever lose.
NSA used to lose regularly, especially on matters of personnel security. There used to be a Judge Green who was in the federal district near Baltimore (if I remember correctly) who took a dim view of the government hiding behind secrecy.
You mean Judge Brinkema, correct?
Yes -- I was writing from memory and didn't have time to look up her name. She's the lucky judge who gets a lot of the DC-area high-profile federal cases -- spies, terrorists, Darlene Druyan, etc.
And you are correct - Francine and Martin blew that case, IIRC. Not a surprise, really.