That is an interesting thought.

We do know Obama (like most presidents) is pretty cozy with the Intelligence Community. We know Trump isn't. I think a coup d'etat or shadow government is too much of a stretch, but this may at least let them work around Trump to an extent.

Also, we're living in interesting times where thoughts like "the intelligence agencies are covertly trying to work around the President!" are actually considered a neutral or good thing by many.