As excellent as Written By the Victors is, I'm not sure the show it's based on is the same show I watch. And I don't think the characters are the same characters. And while all organizations make mistakes, military as well as civilian, I don't think the basic premise of the story would actually fall out the way it's written. The author seems to be following a mind set that I see frequently, and which irritates me a lot. Namely, that Atlantis=good and Earth=bad. Particularly, SGC=bad. And I don't see that at all.
Yes, John and the other people from Earth - but particularly John and Rodney, I think - found something good on Atlantis, something they didn't have at home, but Atlantis isn't the be-all and end-all for them. It would hurt for them to have to leave, as shown in "The Return", but I'm dubious that they would rupture all ties with Earth because of it.
And as for the SGC (or some part of it - I couldn't really tell from the story how much was SGC and how much was the IOA) being collective idiots and handling the situation completely wrong - it's possible, but I think they would have been idiots in a slightly less homicidal way. (Which probably isn't the proper term to use, but I can't think of any other at the moment.) Maybe I feel that way because I like to think people can look at previous mistakes and learn from them, maybe it's simply because I respect our military and hope that they wouldn't make that sort of mistake. In any case, the story's presentation of the military really bugged me.
When I think of John and Rodney refusing to return to Earth and choosing to stay in Atlantis, the only (believable) scenarios I can come up with are basically variations on janusglance's I Feel the Earth Move. There the author gives me an Elizabeth I can see simply abandoning the Pegasus galaxy, and a pressing reason (beyond the presence of the Wraith and a love of Atlantis) for John and Rodney to remain behind. The situation given is all too believable, and reads like something that could happen on the show, if the writers decided to take it in a slightly darker and grittier direction. And the relationships between all the characters, and especially Rodney and John, are note-perfect.
It's a story I wish I could write.