I've always thought of the Deep State as having its origins in the 20th century military-industrial complex. The Eisenhower farewell speech mentioning the military-industrial complex is a classic:

Perhaps not a coincidence -- the CIA was created in 1947, more than a decade earlier... Over time, I think the CIA gradually carved out more and more of a role for itself, including a government-within-the-government (narco-trafficking, gun running, false flags, coups).