My ideas on this the aftermath of an assasin:
Despotism:
With the death of their leader, the nation decends into chaos untill a new leader can emmerge.
Meaning: Forced anarchy for X turns, must form a despotism or Monarchy.
Monarchy:
Similar to depotism but with shorted transition (because yout Heir can take the throne, but still requires time to establish order)
Republic:
The sennate Appoints a new leader. 1 Turn anarchy "transition" phase. Increased risk of culture flip due to independant governing of City-States.
Demo:
Same as republic, but no flip risk, and a Random % of citizens (0-50%) will become unhappy for the next few turns because they voted for the other party.
Commie:
Not to sure on this one. Perhaps a smooth transition with a fixed chance that the new leader will betray your communist Ideals (Tranforms into Despot or Facist)
Facism:
Falls appart for a few turns, but is then re-established as a new Facist regime. Fixed chance that a % of your army not in cities will become part of a "Rebel" AI faction
(Rogue commander attempting to stage a coup at take the seat of power)
These are all just Ideas though, It wuold realy depend on how they set up the Governments in Civ4.(I see this being used as a balancing tool by giving overal "better" governments a higher penalty if you are assasinated) Espionage missions could include both deploying assasins, and training a secret service to protect yourself from other nations. With the effectivness of both increasing over time, and with the completion of certain small wonders like "Secret Service" or "Black Ops Accademy." Certain Civs could also have access to slightly superior assasins. (I.e. the Japaneese reciving Ninjas during the middle ages, but not in any other.)