If Player A and B are at war, and player C joins the war against player B (essentially allying themselves with player A), then the order system I described above can be used... however they will need to take their turn before the person they're attacking if that's what their new ally is doing, or afterwards if it's the other way around. But whether or not they take their turn before or after their ally does not matter, so it shouldn't be a problem.
I hope that made sense... the main thing is, an alliance should be considered to be one player in terms of turn ordering. Of course we can be more liberal than this in some cases... for instance I'm at war with DanD, but since we're far away from each other, there is no need to regulate our turn order.