Well adding a new race might cause implication story wise but never forget the powerful factor that is "Deus Ex Machina" they might find something that brings them back to even greater power or maybe play the old cliché and a new race will appear from the other side of space.

I think it would be fun gameplay wise to add a new race (It also seems like the typical evolution of a RTS game to add a new race)
But story wise it seems wrong to me. But ultimately people buy games for the gameplay (especially when it comes to RTS game) not the story.