Actually, we aren't talking genocide for a major race, are we? We are talking about the taking of one world. It's just an island colony, after all. For most instances in the game, there will be other colonies of the same species elsewhere, so that isn't a true genocide. It's "genocidal". However, when you cannot economically use something, then it is worth being "genocidal" and doing a small bit of research into eliminating a problem on your planned new conquest. What would be more economical for the Yor, for instance? Wiping out every single primate (Human) or merely breaking their 5 most significant nests and having the remainder being a pest on your new territory and costing you resources (resources destroyed or being deployed to exterminate the local troublesome primates)?
It's a matter of economics. If spending a month of research and a month manufacturing of your empire's output would secure a world against lasting issues (ie, survivors fighting a high-cost guerilla world), every non-saintly race is going to do it. Now, if the survivors of your planetary invasion are going to run off to the most unusable bits of the planet, dig holes, and live in them forever without ever causing you any trouble, then the economics would not favor researching a way to quickly eliminate the pest, right? To me, except in the most extreme cases, the economics will guide what is done.
On a side note, if the "survivors" of the invasion run away, find a hole, and never leave that spot, then they are just as effectively killed in terms of the game.
As for more detail and more micro-management:
You will find a very significant portion of GalCiv players against more micro-management. We fans of this game are used to micro-management in TBS games, but that doesn't make the MM fun. Oh sure, in the beginning, it can be. But the 1000th time you've done the same activity, it stops being fun. Just go look at the threads on the new tile system. It adds to the MM of the game. There has been considerable work to bring down that MM, but it still gets boring zoning every planet you take, and rezoning all the alien worlds you take over. In GC1, you only set the governor once, and for invaded worlds, you didn't even do that if you wanted it to use the default build queue (in smaller games, I'd review what was already built, but in the largest games, I wouldn't worry about what was "unnecessary" unless it was early into those larger games).
Again, most TBS players will accept more MM if it results in a more fun game. But if it only adds work but no enjoyment, well, that's not fun. That's where all the invasion discussions start getting into trouble. How to create a more engaging invasion system that isn't going to rob us of the fun of the game. When you play a small galaxy and only need to invade 20 worlds, that isn't to much. But the larger maps can have hundreds of worlds that need to be invaded. GC2 has already increased the MM by a large factor as it stands. Adding more MM to it may push the game into serious grognards only territory. A worry of mine, but a realistic one as the game currently stands.