Is it really plausible that there could have been a super secret federation spy agency that absolutely NO ONE knew about operating in the dark all the way back since the Federation was founded? Especially when there are obviously people at Starfleet Command and The Federation Council which are apparently in on it. I'm sure the Tal Shiar or Obsidian Order would have had to have had SOME idea that there was a shadowy cabal at work within the Federation, especially when you've got Starfleet goody goodies like Bashir running around which would blab about it the first chance they get.