Yes you can. Combat Units can Obliterate the Base:
| Order | Requirements | Hotkey | Effect |
|---|---|---|---|
| Obliterate Base | Must be a combat unit inside a base. | B | Destroys the base, killing all citizens and permanently destroying any secret projects at the base. This is considered an atrocity |
It make sense to sell base facilities first.
Personally, I find obliterating newly captured bases ineffective unless I have solid military concerns (e.g. risk of espionage or a recapture):
- You lose any Secret Projects that existed in the base you've just conquered;
- You lose production and energy; anything above zero is for your profit;
- If you are afraid of heavy drone riots (which can lead to a revolt), better turn drones to Specialists therefore make the base starve and lose the population in a natural way;
- Most importantly (to me): make your victorious units supported from the newly-conquered base! Set Home Base (Shift+H) for them and reduce the burden of unit support from your older bases, effectively improving the speed they are building new units and base facilities. Just keep your eye on your new bases so that they did not exceed the free support threshold that your Govt type provides with.
- Destroying the base (and if there are no other bases nearby) make the territory neutral (or the enemy's). This would trigger Units away from Friendly Territory challenging your Police resources.