I agree that a population should be harder to destroy from space with beams/direct fire weapons. One can wipe out a 1000 mil planet with platforms with 3-4 LC's (armed w beams)in one combat. Maybe the game could be set to wipe out all but the Last 1 million pop with beams, bombs or tropps would be needed to defeat the Last scattering of people. I'm not sure how hard that would be to program though.
I also agree that it is a waste to clear a planet with pop that breathes another atmosphere. What should be used is weapons to destroy facilities only (selectively would be best)
and clear a few of the people if need to make troop take over more likely.