I like a few of those ideas. However,
- Poison City, a pretty straight forward halting of growth for x amount of turns. I think just halting the growth as supposed to causing population loss is not only balanced but a little more realistic. As soon as the locals figure out their water/food supplies are contaminated their find a different source to make efforts to clean the old one up. Also should be subjected to diminished returns. You could add things like releasing viruses or setting off nukes later in the game but the nuke might be a bit over-powered.
- Sabotage Production / City Improvement / Tile Improvement - Also straightforward, I would also make this ability scaling with the rank of the spy too. So, you can either blow up an improvement, or simply disable it for x amount of turns for balancing. Taking out tiles would achieve the same effect as Pillaging and could be repaired conventionally.
- Risk Mechanic, not so much an ability but a display to the player to show how hard it will be to perform a specific action. For instance, say you wanted to blow up a silver mine in Carthage, the game would display how long it would take to do, say 10 turns, and it would have a 20% risk factor because its a precious national resource. There will be guards! Then, later in the game, after the mine is repaired from your previous joy-riding with the mining cart Indiana Jones style you want to take it out again. Now it will take 15 turns and be a 50% risk. You could also make the risk not just tile wide but City/Nation wide similar in the way that happiness is sometimes factored. It would be heightened right after a successful or failed attempt and slowly go down over time.
-Dental