Lambda Wars (formerly Half-Life 2: Wars) brings the struggle between the human resistance and their Combine overlords to a multiplayer real-time strategy setting. The Lambda Wars beta only requires Alien Swarm installed to play. It features 3 multiplayer game modes: Sandbox, Annihilation and Overrun, showcasing the Rebels and Combine playable factions and a full-fledged RTS interface and HUD. There is also a singleplayer tutorial and a handful of singleplayer missions.
There are 12 possible player colors in Lambda Wars (my modest contribution), and here's a spectrum-based color scheme that makes telling allies from enemies easy. This one is applicable to the Squad Wars map sw_woodland that was remade for 3-team gameplay.