[apache]

Actually, I think it should be impossible to completely wipe out a population from a breathable planet, unless you are using plague and/or neutron bombs. Its pretty historic that airstrikes alone, even pinpoint ones, cannot bring a population to their knees. There should be a minimum population on breathable planets that simply cannot be destroyed from orbital bombardments. There will always be those folks in caves, ruined structures, underground structures, and generally just not able to be taken out effectively from orbit. Maybe it should be a bottom limit of 10M, above which you can use planetary napalm to good effect, but once it hits that number, you need to invade or use neutron or plague bombs to finish off the population.
On domed planets, well, they really do not have much chance if that dome cracks, so they should be much easier to wipe out, even using beam/projectile weapons.
I think beam/projectile mounts should not be able to be used on population at all, only on weapon platforms and facilities. Planetary napalm should be limited to population and facilities, and not be able to wax weapons platforms. You figure that a weapon platform is an armored structure that won't be affected by napalm significantly.
Now, on plague bombs, I think they should be changed to kill a percentage of the population, not a set amount, per turn. This would be more logical since a huge population will be hit a lot harder than say, 3 people spread out across the whole planet.
I should also mention that CSM's should be excluded from most of these rules since they are described as using nuclear warheads. They should be less effective at killing population than planetary napalm, but still much better than nothing or beam/projectile weapons, and be able to kill point targets as well. However, they should not be able to break past the minimum population limit.