Spies against installation

For the 2nd time in 15 turns, an enemy spy is on a very important installation. The first time, I countered it by sending my unique spy, and each were killed.

Now how are you supposed to handle that? I guess the mini-game here is more subtle  than regularly spending the citizen you get every 10 turns to remove an enemy spy, right, there is more than that hopefully, because otherwise I don't see how I'm supposed to have enough citizens.