This is something I have been working on too. I am trying to get Spies to be able to assassinate and sabotage as well, making it a Bond-like super-undercover agent. I've had some progress, but haven't been able to quite get it to work yet. A couple other things I was trying was to have catholic priests be able to denounce Muslim priests and visa-versa. Lastly, I wanted all units to be able to "assassinate" assassins and spies once they have been discovered, because there is no good way to get rid of them that I can find.

Like I said, no real success yet, but I am also playing around with the cursor files. It looks like if you cursor over an enemy general, when you have your own spy selected, for example, the cursor changes to the default action of spying. I'm trying to get rid of that default action stuff, and make it bring up an options screen, like how you can choose to marry a selected general or just engage in diplomacy with a princess.

If I have any luck, I'll be sure to post anything I find here.