Another possibility might be to have the facility owner's armor tech reduce collateral damage. It doesn't necessarily mean that every civilization plates all their buildings in top of the line armor, just that improved materials tech probably means the buildings are sturdier.
That would mean that if you invade a pre-TNE homeworld with your plasma cannons and fusion artillery, yeah, a lot of civilians and facilities get blown up, but if you invade a colony of a race with similar tech to your own things survive better.
Edit: Another way of looking at the above solution would be that it equalized the collateral damage per ground unit destroyed. Which is to say, it would mean if a pre-TNE civilization lost an average of 1 facility per 100 troop losses, then a high tech civ would also lose about 1 facility per 100 troop losses, the troops would just be correspondingly more powerful.