I would assume that a turn-based MMO would have a scout system that made you wait on reports before making your next move. Therefore everyone could be playing at once but were forced to wait for the scouts.
I must admit I considered that option myself - then thought to myself: "MMO" - people logging on at all hours of the day and night, some people completing battles swiftly whilst others taking hours, somepeople logging off or dc'd in the middle of a battle. It kind of turned me against too much of an arbitary "stop-go" system of play. Also in terms of the war it wouldn't be unreasonable to have battles occuring up and down a frontline whilst other parts of the line are asleep with inactivity. A hugely successful battle might cause an offensive opportunity if other players also battle in that section to push forwards whilst defenders join in to "Hold the line". In some ways that measure of fluidity would offset the turn-based play nicely imo.
All I can think of is that armies and empires will be long-lasting and old aged - is that workable with your game?
Very true - but given the success of warhammer which is basically a neverending war I think it could be workable. Treat it the right way and it could grind out it's own niche market that supplies tabletop players with a new variation upon their games in the virtual world.