Actually, if you look at donations in the last election government employees in all branches donated over 85% to Clinton. So I'm not sure I'd say overwhelmingly Rebublican by any means.

Trump has been aggressively critical of the CIA and has, to some extent at least, ignored their intelligence briefings. He openly opposes much of what they advocate. I don't think they like him.

Source?

I've always understood the FBI v. CIA conflict as a classic Red vs Blue security alignment. FBI aligned with Defense and CIA aligned with State.