They've totally gone native. There is no doubt about it. Certainly, John has, but I think the others have, too. Atlantis is "home". Atlantis is, according to John, "my city." Rodney is lost and lonely, Elizabeth can't think of doing anything else.
Okay, Carson has turtles, and that's just adorable.
More importantly, John very deliberately burned his bridges. There is no going back for him, not really. There never was, I think.
(And on another note...I posted a story today. In it, I have John playing sudoku - because he *would*. I had not seen the episode yet. When he mentioned sudoku books, I squealed. Loudly.)