That would be a valid point (well, not really, since STiD's based on TOS anyway, so it's not a fair comparison to bring up in the first place)
You're right. The writers just came up with the idea of a top secret Starfleet organization known as Section 31 all on their own and not from any other Star Trek series. You think they also came up with the idea of Klingons having ridged foreheads, having a strong sense of honor and carry bat'leths?