You can just reload the save the game made for you right before you choose the Navi or RDA side. Also, you don't have to complete the sector challenges you already did on the Navi side.
And while I'm here as long as you pick the RDA side the first time, you will always get the RDA achievement no matter what choice you make after the first choice. (you can get a weird ending though although I thought it was weird maybe some of you disagree).
So in short, you will get the achievement this way. I dont even think you can get it any other way.