They should put together a decision system for planet invasions, to allow for liberation. I don't see why a good or neutral civ, or even most evil civs, would wipe out billions of civilians during an invasion. Off the top of my head (and I apologize in advance for a huge post)...
First there should be a good option to keep everyone. There'd be a cost over time, and a temporary morale drop, but after that passed you'd get an influence bonus on that planet. Plus you keep your taxpayers. After a certain number of turns with morale >= to what it was pre-invasion, the people become yours and can no longer be liberated (turns where morale is lower don't count for this total, so killing morale before invading is a good idea). The length of the morale penalty and the number of turns before you own the people could depend on that civ's loyalty stat.
Second, a neutral kick-em-off option, which would be free because the exiled people are taking their own stuff with them, not yours. Population resets as usual, no bonuses or penalties. The planet may be liberated later. After a certain number of turns these people are permanently resettled and liberation is no longer an option. This duration would also hinge on loyalty.
Third, enslavement. You get a permanent production increase and morale penalty. You keep your taxpayers, and get some evil points. The planet can always be liberated later, and will never like you.
Fourth, genocide. Big evil points, population resets, and there can be no liberation on that planet. There could also be some short term, hefty penalties as civilians fight their extermination, dependent on the courage of the that civ.
Last, of course, is liberation, when applicable. Big kudos from the civ it's being restored to, and it's free (the AI might restore planets to strong friendly civs to make alliances). If any alignment changes result, it should be dependent on who you're handing the planet to (e.g.: handing something back to the Korath != good). And, of course, if the liberated civ was wiped out, it gets revived. You also decide whether to exile or exterminate their conquerors.
If you decide not to liberate a taken world, it works as above, except it reflects your actions on whomever the people are loyal to; if you genocide a slave world, the civ they used to belong to will be mad; if you take the good route, you have to win them over from their original civ, not the conqueror. If you exile conquerors from a world that already has an exiled population, both await a return until they resettle, and either could be restored, depending on who's doing the restoring.
I like the idea of liberations... sometimes a friend gets wiped out and I reload so I can pass them a planet to keep them alive. Anything that takes the place of using reloading as a sort of fake prescience, I support.