That is perceptive, and I think it's at the heart of what I see as the differences between genre fiction and literary fiction. In genre fiction, the protagonist has to be likeable, and there has to be a happy ending (believe it or not I am plodding towards a happy conclusion!). The main characters' flaws are more quirks, while in literary fiction there can be a fatal flaw. Billy Budd has that stammer that flusters him and ultimately drives his tragic conclusion. In spite of O'Brien's sarcastic hyperbole, Jamie does have flaws: his sword handling is not adept, he is impulsive, he is indiscreet in what he commits to paper and what he admits to Mr. Turner, the surgeon. None of that rises to the level of a fatal flaw.
O'Brien is oblivious to what could be Jamie's fatal flaw, namely he is queer in a milieu that does not tolerate the expression of that.