I'm not sure. The Spy information states, "Helps Thwart Rival Spies". Does this mean as in performing Counter Espionage missions, keeping your spies in your own cities, or is it simply a missed text deletion for Beyond the Sword?
In Beyond the Sword Concepts\Espionage it states:
"The cost of these Espionage Missions decrease the longer a Spy remains stationary on a tile, but every turn a Spy remains in enemy territory, there is a chance that she will be caught and destroyed. The chances of being caught increase with your opponent's Espionage spending, with the presence of a Security Bureau and if your Spy has recently performed a mission against that tile."
Espionage defense is performed by:
1. Your Espionage spending against the specified opponent.
2. Security Bureau
3. Counter Espionage missions.
4. Apparently/possibly (if NOT refering to Counter Espionage missions or if it is a missed text deletion for Beyond the Sword) the presence of your Spies in your cities "Helps Thwart Rival Spies" as the Spy information says.
In regards to number 4; I believe that your Spies would be better used spending turns on enemy cities to decrease the cost of your eventual missions. The best defense is a good offense.
Like you, bardolph stated, "You cannot stop rival spies from running missions against you, but you can make it really expensive to do so."