The passive missions from Espionage are fairly easy. There's a block you need to remove somewhere in the code and it's mostly XML after that. Look up my Rumours thread if you want some pointers on which files to hack.
The active missions are more interesting. You could use the spell system in FfH and then base the costs and success rate on the ratio of Espionage Points between the two nations. Assassin units ought to gain these "spells" and ideally only at the appropriate techs - so no posioning wells til you've research Poisons. On a successful mission, the casting unit is returned to your capital.
Add a few rare events which simulates successful missions (e.g. The groundwater at the well has been corrupted), so that it is not clear whether or not a player has been the victim of espionage, or has just been unlucky. This is more fundamental in multi-player games. Is someone out to get you, or are you just having a run of bad luck?
Using Spells also gives you the option of giving Civ / Religion / Civic only spells. Followers of Esus could have a spell which, when cast in an opponents capital causes them to suffer a -1 diplomatic hit with all nations for 10 turns. The Elohim might get a spell which improved relations. Aristocracy could have a "Royal Visit" spell which gave a Happiness bonus in the affected city - useful if you want to keep your allies productive during a long war.
Try and keep the mechanics of Espionage away from the player. Espionage should not cost any Espionage Points - just gold. However if you fail, then you should lose both EPs and the unit involved. Another suggestion is to replace the Espionage icon with a Crystal Ball icon instead. In addition you could hide the numbers in the bottom right hand corner of the screen and just display two versions of the Crystal ball. If it is lit up, you know more than you're opponent, if it isn't you know less than your opponent.