Sins Forums
If the population on planets represent native civilians who have joined you as taxpayers, why would they join you after you enslaved thier people and decimated thier defense fleet?
Exactly what's transpiring on the surface is never made clear. The game is very abstract in this way, and you have some leeway to interpret it the way you like. Personally, I view the crew of the colony frigate as an occupation force that "pacifies" the planet and brings it under your control.
I always looked at it as you completely kill everyone on the planet, then send in your own people to start populating it from scratch. In fact I assumed everyone had this genocidal view...
Can you imagine how negatively your population (as a TEC player) would respond to the massacre of the entire Human population of a planet?
Censorship? Of course, what happens with internal affairs of each empire is up for interpretation.
On top of that, who said populations were necessarily human? For all we know, the Vasari could be setting up colonies themselves.
The Devs said that the game takes place in TEC Space, so therefore the population would be Human to a vast extent.
In that case, at least the destruction of Advent colonies would probably would not generate much negative response. After all, they are the "deviants" that were exiled 1000 years ago, and in the words of the narrator of the Vanilla Sins opening cinematic, "... they were lost to us.".
In general, the events of each particular game shouldn't be considered canon anyway - the game, outside of cinematics, doesn't establish much by the way of canon.
Considering time scale, NO, you won't be able to populate a planet from scratch in (an hour)*, no matter how fast your genetic breeding programs are working. That's why it has to be native population based. Getting them to pay taxes... well. You use different methods if you colonize the planet or conquer it, but it's still basically about making the local population pay taxes.
Why so many survive, say, orbital bombardment or the vasari vacuum cleaners... *shrug*
*An hour is probably a bit short, but still, the time scale is obviously fairly limited.
I just wiped out the hole Vasari population in this sector and 2 days later I pull out my fridge and they are all back. 
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