You cannot eliminate the 'quarterbacking problem' in a pure co-op game, where all information is available. A single player 'dominating' the others is not the problem: the problem is that, in such games, there is a clear and optimal path to victory (mathhammer, as you so aptly put it). The 'quarterback's' suggestions must be listened to, because they are actually the best way for the players to win the game. Introducing new player roles will not help you, nor will simplifying the way the information is presented to the players (although I grant you that it will make the game easier to play).
You can 'beat' this by working on the above definition and 'knocking off' particular parts of it, e.g. 'pure co-op', 'all information is available'.
Competition: The problem with making an asymmetric strategy game (i.e. one in which every player has different 'units') competitive is balance. As a hypothetical example, if there is a competitive edge to the game, the fleets of a certain faction might have a slight but telling advantage, that will snowball throughout the game (i.e. better early-game performance). If you choose this path, you will need to be very careful about the stats/skills of the fleets.
Information: There is no way to restrict information sharing between players in a forum community (PMs and all), without their explicit agreement. What about using their capability to exchange information 'under the radar?' Use secret goals: give one secret goal to each player and one to each faction (shared between all players of the faction). Allow them to share information via PMs. See the game explode with misinformation and misdirection. There is nothing that can stop a player from claiming that he needs to follow goal A, but how can you trust him? What if a player betrays his faction goal to the others? What if...
Then, on game end, award points on successes and see who the winner is (if we've managed to defeat the Hierarchy).