Intrigue is really the worst new concept of the game. Coup is incredibly powerful, and it even works on Capitals. With a teleporter Satellite, you can instantly reinforce the captured city with a large army.
So obviously it needs to be counterable. If there was a sure way to do this, it would be overpowered.
However, a counterspy is so incredibly strong, all you'll ever get to do is Siphon energy. All the other highend abilities are just out the window at this point. Intrigue is really only good for embarrassing a new player who doesn't get a Spy Agency (I'm amazed you can tell who has the spy agency from the diplomacy menu. It's a bloody SPY agency, it wouldn't broadcast its existence to the entire world. This is almost as stupid as being able to check how much research per turn someone is generating)
There's also standard buildings that prevent any detrimental abilities by hard capping intrigue at 3.
The whole intrigue system needs to be redone from scratch. I don't really see anything worth salvaging there. The game in general needs to be far more conservative with throwing information around. I'm a huge opponent of the demographics window. If you want to know how much military someone has, spy on him. Don't look it up on a chart.
The only decent part about the spy is the detailed city info window you get after establishing a network, and that part is actually broken, I usually don't get to see that window on 1 out of 3 cities.