Actually I think a CIV MMO could be many very different things.
I doubt that a Wow-like Gameplay would lend itself very well to a Game which has Civilization in its name. I mean players banding together in order defeat computer controlled monsters in order to aquire new and shiny equipment. That doesnt sound too civilizationish
I think that a Civ MMO should be based on the Idea of many (hundreds/thousands) people forming a nation. Upon the creation of his game-avatar a Player might choose a Profession. Im thinking of soldier, merchant, craftsmen, politician.. here. Each Class/Profession can basically roam the world, kill animals and stuff. The difference lies in the specialisation. Soldiers are best at warefare, Merchants and Craftsmen might be best at gathering ressources or building things (weapons, buildings, tradegoods)
In WoW you have two different Fractions (Horde/Alliance), in Civ we could have many different Fractions. One for each Nation. these Nations would then struggle for control over the various city sides. That means Players engange in PvP-Combat of some sorts. The Equipment (aka Weapons) and therefore the combat strength of each player would be provided be craftsmen of each nations. The further developed your cities are, the better your weapons. In order to help balance things out the game could restart every other month(or year), starting in the stone-age.
The major aspect of the game should be to encourage the buildup of communities. The Players should be able to shape the world according to their actions..