I dunno about retconning, (upon close examination it certainly feels possible) and frankly I could care less if it means John is actually as smart as he appears to be. Sort of.
Anyway, that's not the point of this. Two things are bothering me and I'd love to hear your opinions on it:
1: Did Derek actually kill Jesse? The cut-off (thanks for zero gratification, producers) leaves us hanging without a real idea of her fate, although we can of course speculate. To be honest, I'm not quite sure if he had it in him. Unless John was *really* persuasive, or Derek was only humoring her the whole time, I don't know if he really would have gone ahead and killed her in cold blood as she was running away.
In fact, it almost seems as if he was letting her go. This is a man who can quick-draw and shoot a man in the head PAST a very important hostage without breaking so much as a sweat. He could have downed her easily had he the piece of mind.
But at that range? On the stairs? With a pistol? I don't fully buy it. Of course, stranger shit happens on television.
So, while I am very skeptical, we'll assume for now that he killed her, which leads me to point two:
What was with John's breakdown at the end? My theory is this: going with the above theory, I'm guessing John ordered Jesse's killing, but couldn't do it himself. Therefore to make himself feel at least somewhat better, he let her go only to have Derek do it for him. Thus the crying at the end. He's guilt-ridden over having essentially ended another human life.
It would be repetitive to have him breaking down because of Destiny and being the Leader, because this is trodden-on territory and he already had a scene very much like this in Goodbye to All That.
Or it's merely because he's finally grieving for Riley and his essential involvement in her murder. Seems a little late for that, though. I think it's much stronger dramatically for him having to accept the idea that sometimes he has to order the deaths of others to achieve a goal.
What I personally think: Despite my reservations, Jesse probably bought it. And John was grieving for Riley, finally. Sort of silly, but there you go. Your opinions would be appreciated.