I've read in several places that the fictional story was made due to the Cold War. The original plan was for a simulated missle attack on American ciites, with one base on the Atlantic and another on the Pacific with the third one in the center. There were concerns though that a game that struck that 'close to home' like that would hurt sales, cause a panic, and give a lot of bad negative media attention. This was in the early 80's, mind you, when the Cold War was heating up again and Regan was in office. Even the creator of the game said he woke up several times from nightmares of a nuclear attack when programing the game. So the back story was changed to a more generic fictional sci-fi one.
It makes sense that Atari would change it for a family friendly home console. I was flipping through one of the old Atari catalogs, the one that divides games into categories.
Missile Command is under "Space Station" instead of "Combat Zone". In reality, Missile Command IS a war game, not a space game.
Now that I think about it, I do remember my friends mother not wanting him to get Missile Command because it was about "Nuclear War" and truth be told, she was right, no matter how Atari may have wanted to sugar coat it. I think he did eventually wear her down and he did get it though