I believe the two nations going at war would summon sort of 'Codes of Conduct' during battle stating viewpoints they both see as unjust in war. Otherwise a definite set of rules is hard to make. Although, one rule/regulation we could go over is inactivity time. I know during my time playing defense on Oto, village battles can become lengthy due to a single or multiple parties slow response time. Sometimes taking weeks to get a single response in dire times. So maybe a ruling set to make it acceptable to skip over a certain players actions over an x amount of time and cause them to be 'auto-hit' or dealt with in accordance to RP, as if they went MIA during the mission or whatever. Or we can discuss how one would go about and wage war between certain nations, since an overall siege of a village/country isn't necessarily war; rather an aggressive take over.
Then there would be the matter at hand during a war, some nations would restrict access to their village from foriegners and allied nations of their enemy. Causing a whole mix of RP to be done. I am truly trying to test out how a war would be done, NPC wise so its much easier regulated, but It certainly would be fun to organize and construct one with the community as well. I agree with Eric, that we should indeed have a certain set of rules/regulations of how, as civil keyboard warriors to go about war.