Your example of Japan actually makes my point:
1. The Japanese *did* surrender, this is a historical fact. It is true that the Japanese government made a lot of noise about fighting to the end beforehand. I think it reveals how some aspects of Japanese culture have been trumped up to legendary proportions that even in the modern day people take this seriously... Soldiers might fight to the death... if they have no alternative, but civilians are another matter entirely. As a rule, take any propaganda or last ditch plans made by governments losing wars with a grain of salt.
2. You should note that the whole reason that we used nuclear weapons, even though this meant tipping our hands to the russions, was that a land based war of attrition was considered incredibly undesirable. Again, after the war we took steps to gain the cooperation of the existing Japanese government, sparing some from war crimes trials, most notably the Showa Emporer. Similar tactics were taken in Europe with the nazis.
For an example of how costly and stupid demolishing an existing society is and building up a new one up from scratch, you need look no further than our current war in Iraq. When we entered Iraq the first thing we did were
1. disband the army
2. fire the police
3. fire anyone with connections to the baathist party i.e. anyeone with experience running the country
We didn't exactly go in looking to fight a war of attrition with the local population... but after you do the first 3 things, the other thing follows whether you like it or not.
If you read a little machiavelli, or pretty much anyone else who knows anything about politics and war, you learn that the proper way to take control of a state through force is to leave as much of the government untouched as possible, keep the local officials and laws the same etc, but to kill off everyone in the top echelons of government who might have a ligitimate claim to power, and also their families if power is transfered along hereditary lines. Some people favor killing the ruler, and taking his descendents as de facto hostages back to the home country while a puppet government rules in his name. I believe the japanese did this to the korean monarchy at some point...
I always thought that taking the ruler of a foreign country hostage, would be a good element for some of these civilization style games. It would be a good way to create satellite states.
