A few additional thoughts:
1. Unless they continued filming more scenes of the zombies fighting (and the end result) at the time, there has to be some kind of instant reset, since I can't see them spending all the time and money (and ...um...continuity checks...) to match the final "epic" battle after however many months before they start shooting again. At least, not to pick up exactly where they left off. All those extras, makeup, multiple camera angles....
Or maybe the missing scenes (like the angies and Cas driving the Impala) will be used next season?
2. I'm going to do something very unusual for me and *maybe* defend Sam here. After all, they've always shown him to be a dead shot (except when he had the Trials sickness), and since they seem to be recreating so many favorite scenes from old eps, maybe he was actually *planning* to shoot Chuck in the shoulder (the way he shot John in the leg to get him to fight off Azazel.) Of course, Jared didn't play it that way this time--more like, "oops, I missed," so it didn't come across as deliberate. (Maybe they didn't tell Jared the reason he was supposed to miss?)
3. I think Dabb never really had any ideas of his own and just "borrows" them from other shows (including this one). Not to insult comic-lovers (my own experience with comics is from way back when they were all 2-D heroes and villains) but it seems to me that that's what Dabb's expertise is--writing 2-D characters with 1-D motivations. I'm hoping this was his swan song and that's why the big thumb-in-the-nose to everyone. But I can see him using Jack to Save the World and restore everything, ending with the happy Winchester family eating dinner in their suburban Kansas house.