I counter that by saying Id like to think that The Blackstaff would be capable of keeping the secret, and unless he is very intentionally lying to Harry, then he created the GC specifically because he was not getting the Merlin's support the way he thought he should. I just dont see either of them going the GC route if they were working together on it; there'd be nothing stopping Eb from simply establishing his own group of Wardens like I assume the Brute Squad was for Simon.
First, I agree if the Blackstaff wants to keep a secret, he will most likely be able to do that. Including from the Merlin. I think the Merlin knows because he isn't dumb. (don't get to be leader ... bottlecaps, so on and so forth) Merlin is at the head of a powerful Magical organization, who granted is short staffed, but is still a major power in the world. He should have the intellect and knowledge to see what is going on.
I think there is a difference between supporting something and acting on it as the Head of a Major Power. Take in to account the scene in the Worry Room in Changes between the Merlin and Harry. They all think the peace is a joke, but have to put on the airs of trying. Same thing could be said of this. Merlin needs to put on airs officially that there is no BC, hence there is no need for a GC to combat them.