What would happen to the population?

They kick out the former government and some local party takes over?

Hmm, good question. I would suppose that they would be the entire reason the planet revolted in the first place, what I see happening in my "mind's eye" is that the population of the planet reaches a "critical mass" of both unhappy "native citizens" and rebellious alien citizens. And the aliens would defect the planet to a localized hostile government and promise the other citizens full citizenship in the new "world order". So to say. I dunno just imagine what happened during the American revolution happening on a global scale during galactic conflict.

I'd imagine the native civilians and citizens living on the surface,along with the factional citizens living in atmospheric cities,would be disgruntled with the ruling faction because of propaganda would, when the Planet Allegiance gets very low(like about 30-20%), they would slowly start attacking low level Government facilities like post offices,banks,etc then it would slowly progress up to medium and high level Governments facilities and then, finally, the dissidents rebellious,terrorististic actions would get to the point that the Aliens would get so fed up with it,that they would just say"screw it!" and abandon the colony.

I think for all intents and purposes for the game this is what would happen. BUT in a real world situation martial law would be declared and the military would become involved in trying to suppress the rebellion. For prime examples just look at what happened during the French and American revolutions, as well as the Chinese rallies during the late 80's - early 90's.

 I know I'm delving into the Real world,but what does Martial Law entail?

Martial Law varies in certain situations and depends on who is enforcing it. Imagine what was going on during Nazi occupation of Europe, specifically France who immediately surrendered to the Nazi's without putting up a fight... the Nazi's didn't particularly disassemble the government (although it was under intense scrutiny and jurisdiction of the Nazi party) and didn't really abuse the citizens of France BUT they were closely watched and harshly punished if there were any "suspicious" activities or if the occupying Nazi's felt that certain person's were conspiring against them for any reason.

While that is the EXTREME form of Martial Law, there are other examples, like US occupation of Iraq after OIF. Or even the US occupation of Japan during WW2.

Yes,but the ruling faction would probably imprison the rebellious colonists and confiscate their property and possessions and they would probably execute a few rebellious natives,which would lead to further unrest and plus the planetary ground forces would probably join the rebels and realizing the colony was lost the ruling faction would destroy their own infrastructure for whatever reason.