I have a feeling that quite a few fans will take the first half of this episode personally. The writers were definitely tossing out a few well-aimed shots at certain, shall we say, "overly enthusiastic" segments of the fandom. They weren't above poking fan at themselves, particularly some poorly received episodes and their eternal ratings struggle, but they were mainly taking shots at their more strident critics with just the right mixture of tolerant affection and scathing mockery. (The slash conversation, in particular, was classic: "They do know we're brothers, right?")
In the grand tradition of Whedon, this was the classic bait and switch. The first half of the episode felt like a gimmick, tossing out the meta relentlessly, and there was no sense of where it would go. If anything, I was content to sit back and see if the gimmick could last a full hour. The second half, however, took a decidedly darker and more meaningful turn.
I love the idea that Chuck was a prophet of the Lord, and that his barely-regarded "Supernatural" novels were eventually going to be hailed as "The Winchester Gospels". Considering how the covers and the prose took severe liberties with the brothers, even while describing events with fair accuracy, I suppose that's an indirect homage to those who question the motives of the biblical writers.
But this is also indicative of something that should be apparent by now: the Brothers Winchester are expected to win. One doesn't write a gospel about someone who fails to forestall the apocalypse, after all. There would be little need for gospels at that point, anyway! Prophecy appears to show that Lilith falls to a greater threat, and the Brothers Winchester are wrapped up in that.
After all, Zachariah has already mentioned that Dean is supposed to serve a specific function in events to come, and Sam is also wrapped up in it. Lilith wanted the Brothers Winchester dead for a specific reason. My suspicion, with so little time left, is that this encounter prompts Sam to accelerate his sessions with Ruby, so he can gain enough power to take down Lilith, and this in turn makes him the very threat that terrifies Lilith and leads to her demise.
This is corroborated by Chuck's final scene of the episode, where he receives a vision of something awful for the Brothers Winchester, something he desperately wants to warn them to avoid. Zachariah, however, makes it very clear that it cannot happen. This suggests that the angels aren't just there to shepherd Dean to his appointed destiny; they are also there to ensure that the outcome is as foretold.
Which is why I still believe that Sam will go dark side in the process of ending the threat of Lucifer's release. (Or perhaps Sam's conversion is itself one of the final seals.) Sam then takes on his destined role as the Antichrist Superstar, and begins to implement whatever it is that Azazel was trying to achieve (something from earlier in the season that hasn't been mentioned in a little while). At this point, it would be a bit of a cheat if the writers failed to pay off what they've been building towards since the second season.