Civil war in Galciv 2 is represented only by the Fundamentalist event and a very, very rare dicontent event that I have only triggered once by setting my morale to 1% to see if it would trigger, wherein the population loss was more damaging then the defections.
I propose that, for each percent under the red numbers of happiness, there is a chance that a planet tile will be disabled with a homegrown spy. When all the tiles are taken up, the planet breaks away or joins an ongoing secession movement. This way, discontent is penalized, civil wars can happen, and espionage and counter-espionage is made more usefull.