I like your selection of actions, it will give you a wide range of possibilities. I also like the idea of having a role for your spy and an additional stronger action if your spy survive. However I would like to have those actions also for your counter-intelligence spy.
The Counter-Intelligence:
So you suggested that counter-intelligence should be like in the vanilla game, by just defending spy actions of hostile spies. This would mean that only your enemy who stationed a spy in your city for instance, would profit from a wider range of possibilities for his spy. The enemy could decide that because of your wonder in progress, his spy should try to sabotage your production. You on the other hand would have only the option to deploy a spy in this city to defend your progress.
So why won't we say that you could also select an action for your spy, by choosing one of the actions you posted above, but this time by selecting Sabotage for your counter-intelligence it would mean: reduction of hostile spy actions like in the vanilla game, plus a reduction of the possibility for being successful of delaying your production.
So you would say to your spy: "Hey watch out for enemy spies and keep an eye on hostile spies who want to sabotage our production." This would then also work for those other written actions, like Thief, Instigator, Manipulator etc.. So you will always have the bonus agains hostile spy actions, plus a reduction for the special ability of a hostile spy. This would make the spy system more interesting, because when you select "Keep an eye on Saboteurs" and your enemy chose a different action for his spy (because he is not interested in your wonder, but your gold), you can be successful against a spy action in general but not against his special ability.
To spin this idea a bit further:
By entering the spy menu, the displayed potential of a hostile city is being influenced by the following factors: Is a hostile spy deployed in this city? If yes, what is his chosen action? If similar to your action, the potential will be reduced. This would make the spy system more challenging by a more hide and seek like system. In my oppinion it would be fair enough for both sides, for the active spy and for the counter-intelligence.
The concept art:
This is what I have in mind, I made it with Paint, because I currently have no other program for this.
View attachment 389540
An additional button has found it's way into the spy menu, where you can select the action for your spy. Either by pressing the button and choosing the action in a new appearing window, or by having a dropdown menu instead of this button, you could choose the action for your spy.
It would be helpful to have a mouse-over descriptions for the different actions by showing just the text of what Finarvi wrote:
1. Saboteur: Chance to kill

. Eventualy delay current production.
2. Thief: Chance to steal

. Evetualy steal technolgy.
3. Instigator: Chance to inrease

. Eventualy make city resist.
4. Manipulator (only available in city states

): No changes here.
5. Diplomat (only available in other players'

capitals): No changes here.
6. Counter agent (only available in your cities): No changes here.
The text will slightly differ from having an active or a counter-intelligence spy. The potential to the right side will be influenced by having an enemy spy in the foreign city and additionally if he also chose the same action for his spy. This would mean on the one hand, that you could possibly find out what action a may existing spy has selected, but on the other hand each time you change your action there will be a delay like in the vanilla game..
So what do you think? Btw. I am not able to press anything of my idea into code or into the dll, so I hope that there would be some guy who could do this instead of me..