Have you ever heard of the tier system? It worked. Was Lucas or Lucasfilm obligated to follow the EU? No. However it the EU was integrated together far better than Trek Lit was for most of its(Trek) existence. You hand Leland Chee and the Holocron, Pablo Hidalgo, and Sue Rostoni, also Shelly Shapiro at Lucasfilm they kept everything tied together.
It did work for the SW EU, but trek never adopted it. Canon in trek is a much simpler concept, if it happens on screen it's canon, if it happens elsewhere it isn't.
That doesn't detract from the quality of licensed works, nor does it guarantee the quality or the consistency of the canon. It it nonetheless the way the franchise works.
However, I wouldn't be surprised if there was something out there that just uses the CIA as its diversion.
I do wonder if this is possible in the current day and age. My cynical side pretty much assumes that there will always be secrets beyond those publicly acknowledged to at least exist, my practical side wonders notes how difficult keeping those secrets seems to be in this day and age. Part of the demystification of the CIA, MI5, Mossad, whoever, rests on the fact that we have a pretty good idea what they do and how they do it these days. The specifics of any covert operation may not be public, but the modus operandi is by necessity much more open to scrutiny, precisely because the world has far fewer shadows and far more exposure these days.
Bad things still happen, but our perception of those things is based more on the news, the internet and a much more globally aware public than it is on movies, novels and fantasy.