Based on the title, I thought we were going to see the "Supernatural" version of the Rapture as described by evangelical Christians. After all, it is a fairly well-known aspect of many interpretations of the Book of Revelation. With Lilith breaking seal after seal and bringing the world closer to apocalypse, why not?
Instead, this was a story about Sam's growing addiction to demon blood and the consequences of being host to an angel. Both elements were surprising in different ways, but Jimmy's story was clearly the most unexpected. Misha Collins fans had to love this episode, because the actor was finally able to show some range, and he was on-screen more than the Brothers Winchester.
It was fascinating to contemplate that a vessel so willing would end up regretting the choice. There are a couple of ways to look at it, and I suspect it will have much to do with the mindset of the person making the interpretation. Those looking for the silver lining will recognize that the moral of the story is: be careful what you wish for. Uninformed choices can have terrible consequences. Jimmy couldn't have known what hosting Castiel would entail, and one can see how the disconnect between expectation and reality would lead to a crisis of faith.
Of course, the more negative interpretation would be that the writers are trying to depict angels as uncaring and even sinister, thus suggesting that Jimmy's conclusion that his faith was based on a lie is the intended message. I think that would be a short-sighted and self-serving interpretation. In essence, Jimmy volunteered to be a soldier in a war he didn't understand, based on trust and faith in the rightness of that war alone, and the reality of the situation tested his faith. Given that the loyal angels have been shown as willing to kill human beings to get the job done, that's not a surprising reaction.
Sam is much in the same boat as Jimmy, though he doesn't have the excuse of stepping into his situation without a clue. He just didn't think things through properly, and Ruby has been manipulating him for quite some time. If there's an amusing side to this, it's how obvious Ruby was from the moment she arrived on the scene. She told Sam that her goal was to back him as the Antichrist Superstar and convince him to assume his role, and that's precisely what she's been doing.
Yet, just like Jimmy, Sam went into the situation with all the best intentions (gain the power, avoid the temptation), and he got in way over his head. Dean and Bobby did exactly what one would expect them to do: contain Sam until they can find a way to bring him back from the abyss. Of course, something is going to go wrong, because it always does, and the apocalypse hasn't been canceled yet. Which mean, for "Supernatural" fans, that it's time to prepare for another jaw-dropping season finale!