I thought the "life changing moment" was that the Sheppard in "our" reality saved the medic and the one in this reality didn't.
I think considering the time period involved Shep was already on an SG team by then and wouldn't have been anywhere near afghanistan.
Wait, am I confusing war hero team leaders?
Was Cam the one that "disobeyed orders" to save someone in Afghanistan?
I vaguely remember a flashback episode that actually featured one of the characters fighting in Afghanistan to save the some guy... I just assumed that it was Shep and that it was an Atlantis episode.
Anyway, if Shep came on board during Atlantis and the series follows real world dates, it would have been 2003/4... which gives him plenty of time to do a tour in Afghanistan... or at least see action there.
Here it is:
John Sheppard is an experienced and talented pilot in the US Air Force, though his reputation was somewhat tarnished when he disobeyed a direct order in Afghanistan in an unsuccessful attempt to save the lives of several servicemen. He has experience flying AH-1 Cobra, AH-64 Apache, OH-58 Kiowa, UH-60 Blackhawk helicopters and CV-22 Osprey tiltrotor aircraft.
That's from Wikipedia. So if he was unsuccessful in both realities, I suppose in "ours" he decided to mope around in Antarctica rather than quit and move to Vegas.