Hmm, well that's the tricky thing, you can justify all sorts of extraordinary and awful practices in the name of achieving a "good" cause (many news headlines come to mind). It's kind of disturbing, but also interesting to think about in Dominions terms since you would be the one responsible for said acts.
As for what good and evil mean, I think we're stuck with using the commonsense ideas we've inherited today to a certain extent. Of course if we tried to put ourselves in the shoes of a civilization from 3000 years ago, it would probably be different, but I'm not sure I'd want to be a barbarian.
Hey this gives me a new idea: Civilized people vs the barbarians. However this is also a rather big can of worms. Both Mel Gibson's Braveheart and Ghengis Khan come to mind. Maybe EA nations could fight LA ones or something.