Broccoli, the cost of repairing is directly proportional to the asset damage of the targets you hit. If you hit targets that provide most of the war index damage through means other than asset damage, you're good.
Maybe the values changed, but last I checked these were the asset damage value of targets:
Capital: $1T
City: $300B
Town $50B
County: $10B
Everything else: $2-3B
You can easily achieve minimal asset damage in a country you intent to keep by hitting only these targets:
Painting: 30 points.
Fortifications: 50 points.
Corporations: 20 Points.
Even if the C3 has, say, 100 Forts and 25 corporations. The asset damage of hitting all of these will be less than that of hitting 1.25 cities (imagine damaging the second to 25%).
As far as the rationale of hitting corporations, the cost of setting up a new corporation is offset both by the money you earn by destroying an older corporation and the asset damage savings of not hitting a population center. Additionally, the corporation you build will likely be a better type than the previously existing corporation.
This is even true if you'd just build the same corporation because the points saved from asset damage (essentially, the points earned by doing corporation damage to the war index) mean very real savings to the cost of repairing war damage, given that C3 corporations will essentially be equal to a new corporation in terms of upgrades. Additionally, corporations generally take fewer missiles/bombs/shells to destroy than cities per war index point meaning you further save money on that end.
As far as a general principle to apply when attacking a country, get all points via the cheapest method in terms of points per sc$ (taking into account ammo cost, repair/replace cost), then the second cheapest, then the third cheapest, etc.
Which means... always get the maximum points possible from painting. The other stuff is a little more fluid.