… and then he says “Excuse me?” ???? *aaaaaargh, cries*
Jack, you idiot!
I think this reaction was dumb too. To make it better, my headcanon is that he reacted that way not because he was scolding her, but because he was so surprised. He’s known Carter for almost seven years and as far as he knows, she’s only called him Jack once, years ago, and she was possessed by Jolinar at the time. (I don’t think he was conscious enough to know Sam called him Jack when they were stranded unknowingly in Antarctica.) The only other times she’s called him Jack, it wasn’t Carter at all, but the AU version of Samantha Carter who was married to him. So I choose to believe that his “Excuse me?” didn’t mean, “Why do you think you’re allowed to call me that, Major Carter?” but rather, “Did I just hear what I think I heard!? Dare I believe that you are actually talking to me as a friend and not as your CO?”
Sam, being the perfectionist rule-follower that she generally is, would of course have interpreted his reaction to mean “What makes you think you can call me that?” so she apologized and reverted to “sir”. Also, she might have been a little mortified that some of her private thoughts slipped out when she wasn’t quite in control, so her immediate reaction was to deny deny deny. “What, sir? I don’t think of you as Jack in the privacy of my mind, no sir, why would I do that, why would you think that, sir?”
After all, Jack’s reaction after her apology was basically to shrug it off and beam happily at her and then they gazed longingly and lovingly at each other for a while. So it’s clear he wasn’t really bothered; he was, in fact, secretly stoked that she called him that, even if it was only by mistake.
THAT IS MY HEADCANON AND I’M STICKING TO IT. Because they’ve been friends and teammates for years and she’s been missing and he’s been out of his mind with worry and she’s medicated and half unconscious, and him scolding her for not showing the proper respect to her superior officer would be extremely dumb and I refuse to believe that was the intent.
Don’t worry. Your headcanon makes sense.