To be honest your question is to vague. I can visualise the slavery kind of, but what r we suposed to do about. If our planet screen was more like civilizations city screen, or at least kind of like how their population works then we could implement slavery by taking population. This would require a slaver ship. Maybe the citizens could be tax collectors, scientists, artists, or workers. Then slaves would be only workers. This would have to have some of the population surviving after invasion.

     We could say that a newly invaded or defected planet would have a different status than one that was part of the empire. I think that slaves should be cheaper than everyone else.

To be honest, I just want a system where my 100% good race doesn't have to, for all intents and purposes, commit genocide every time it invades a planet.

That's not really my point. I just think it's kind of ridiculous that I can be playing the Altarians, with a generally pacifist policy, pursuing a diplomatic victory, and still (for all intents and purposes) have no choice but to slaughter the entire population of any planet I do invade. Introducing different populations could help fix the cognitive dissonance.

The population value is not the actual population, but the amount of citizens paying taxes to your empire, these citizens don't necesarily have to belong to your race, but slaves will definitely not pay taxes, so won't be counted as part of your population, and after a conquest initially you will only get taxes from the occupation forces you sent to that planet. The Good races would slowly integrate the imprisoned former population into their own society, or ship them off to worlds belonging to their empire via a neutral third party, or during peace-time.