I don't believe super projects or galactic achievements can be destroyed in invasions. I know I reloaded the same game about 50 times in DA trying to do that to a MCC I really didn't want to have. No luck, if you absolutely MUST destroy one of these projects, you can only do so by rendering the planet uninhabitable (by abandoning the colony) or destroying the star.
I usually buy the techs necessary to keep most buildings when I invade. I may not want to keep that slave pit, but it will speed up building its replacement.
As for tactics, I usually disable morale buildings and use information warfare. Yeah, it's expensive, but it's usually a one-transport kill, and often I end with more population than my transport started with. The planet recovers far more quickly.