Anyway, we definitely can protect installations from stand-off weapons: CIWS systems like the Phalanx can shoot them down these days, and they're relatively cheap. It's not perfect protection - eventually one will get through - but it does raise the cost of a successful attack substantially.
Ideally, in war, you destroy their military, or at least damage it enough for the other party to concede and discuss peace terms, and leave the rest alone.
WW2 was, I believe, the last war where they went for complete destruction of infrastructure, industry, and civilians. The Allies firebombed Dresden and nuked Hiroshima and Nagasaki. It is estimated that 50-55 million civilians died in WW2, of which part due to disease and famine. No conflict since has had that high a civilian casualty rate.