I don't think it could use the same slot as MC's. The reason being, there is only one slot. If you sign a friendly agreement and suddenly get rebels, then I WONDER WHO DUN IT. There is also the issue of needing trade agreements with friendlies. You can't get an agreement with enemies, naturally, so you can only mess with allys.
For Syndicates, maybe makes sense, but I wonder how viable screwing with someones politics will go over as a smaller empire. As it is, the crime addition is a debuff to the owner.
Other issues include using a single espionage slot on a planet would not allow multiple players to interfere with one entity; you would have to fight over the right to sow a little dissent in the current setup.
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For this to work (I thinks its a pretty good idea), we would need a special UI per rival planet for building expensive projects/fronts. It would need to be only viewable from the player and would be effectively independent of all other players to allow overlapping espionage.
Detection would be an edict that once activated perhaps had a chance of finding a random empires UI so the player could see whats being sponsored to hurt their planet. Then follow up edicts to shut down different projects/fronts would be usable.
For consistency, I would imagine only being able to build on rivals planets.