By Civilisation do you mean organisations or cities built with heaps of players inhabiting them?
They're both fairly similar in outcomes, resources and time are lost in either case. An org could grow back a lot faster (Depending somewhat on the leadership) while the city would take a lot more to rebuild, if it wasn't scrapped by the victors/survivors.
Now, Say COPS and HMMR go to war against each other, they're spending a crapton of resources and time fighting each other, this can give a smaller group like DUA the advantage it needs to build up there resources while the two larger orgs are at war. War could easily mean a complete powershift in organisations/civilisations.
(Examples of orgs are just examples, not implying anything).