I'm pretty sure a windows live id is something completely different from Games for Windows Account Support. You need to create a new Windows Live Account. Microsoft (and steam as well) have one account for the game and another for support. This is a security feature (If your game's account is hijacked, you can still report it with the other account).
In any case, you can run Fallout 3 without logging in to GFWL. The only difference is that your saves are in a different folder and you don't get any achievements.