The Blue Prometheans do not work with the Covie becuase they are just to protect the Didact and any sensitve materials, places, objects etc. While the Orange Prometheans are out to face the threats, as Zaguroth pointed out, the Orange ones only side with the Covie part way through the game and only for a specific reason, to kill the humans. So in essence it will end up being a 3 way fight, Covie vs Human vs Promethean...most likely of course