--Major update: ground combat--
As I should have intended:
Let say planet B has a population of 10B. that means, it provides 10m soliders, which is a large amount.
Let say A invades B and A kills all 10m soliders. The population will, in any case, decrease by 100m, and # of manufactories shall decrease by 1000, which is 10% of it. As 1% of population perished, so loyalty will decrease by 1x10=10%. If B holds, it is the damage received by B.
Now, of course, since A wins anyway. If A choose to occupy, It should kill 10% of population, without additional loyalty penalty (that is still 10%). In addition, since infrastructures suitable for the past regime will be disbanded, manufactories shall decrease by an additional 1000. In addition, it loyalty would decrease by another 50% for petty resentment towards their true masters. That means usually it would be left at less than half, and probably very near zero.
Of course, They can just hold a massacre and exterminate the unruly population. In this case, 80% of remaining population is 7.2b, leaving 1.6b who value their lives. 45% of the original manufactories, similarly, will go poof, probably as secret police like to blow things up to intimidate people.
So, in a nutshell:
1. -RULE AMENDMENT- Orbital bombardment may bring down loyalty. Ask anyone "who owe their large pensions to Wernher von Braun" how V2s feel.
2. -RULE AMENDMENT- Damage to manufactories from peacefully occupying is now DOUBLED not 10-folded.
3. -RULE ERRATA- 80% population, 50% manufactories for extermination.
4. -NEW RULE- 50% of Defending armies attack strength is affected by loyalty value. So if they are completely demoralized by bombardment (0% loyalty), they only attack half as effective. 50% loyalty will mean 75% effectiveness. This is to improve the effectiveness of orbital bombard without killing too many.
Rules will be updated immediately.