As soon as this episode began, it was clear that this would be a major turning point in the season arc. I haven't always liked the depiction or treatment of Anna since her original entry into the story, but it was very clear that her presence marked a mythology-heavy piece of the puzzle.
The writers had to walk a very fine line in this episode. Anna's plan is essentially the familiar "Terminator" plot: killer from the future goes back in time to prevent an obstacle to its plans from being born. The critical flaw to that plot is the needless complexity, especially when the assassin could essentially arrive at any point in time and make the necessary changes. Also, the more often the assassin fails to make a swift, clinical move to execute his or her plan, the less effective the plot device.
For much of the episode, it appeared that the writers were falling into the trap. Anna had several opportunities to kill Mary and John, even without Uriel's help. Too often, she seemed to hesitate, when her righteous surety wouldn't have allowed for it. Had the Brothers Winchester managed to defeat Anna and Uriel, then it would have been a deeply dissatisfying episode.
In that scenario, the story would have required that Mary and John know about the hunters, the future, and their own fate before much of it came to pass. While there's a certain power to the notion of Mary and John choosing to accept their fate, as a compelling act of long-term sacrifice, it also would have been rather messy in light of the overall series narrative. (Though, the idea that John Winchester might have been led to the hunting lifestyle by Sam and Dean would have been delicious irony.)
Instead, the solution was near-perfect: the long-awaiting first meeting between Michael and Dean. Not only did Michael resolve the problems with the "Terminator" plot, but he allowed the writers to have the best of both worlds. Sam and Dean were able to have all those incredibly awkward and unsettling conversations with Mary and John, yet have it all erased by an established reset button that wasn't. (After all, Team Free Will still remembers what happened.)
On the face of it, Michael's argument is deeply compelling, and adheres to one very popular religious interpretation of human existence. In short, there is a grand design to everything and for everyone, but the perfection of the plan is that the pawns don't ever realize that they are playing a destined role. Free will, the power of choice, is illusory; all the apparent choices still lead to the intended outcome.
It's not hard to understand, especially when the destiny is decidedly harsh and painful, why such an interpretation of existence would bring despair. And it's even worse when all the evidence points to that very conclusion. Mary came from a long line of hunters; John's family line goes back to Cain and Abel, the original story of Brothers with Issues. Dean had to feel as though the weight of predestination was coming down on his shoulders.
But here's the critical part: the entire plan hinges on a choice. In this case, two choices of identical nature. Michael and Lucifer cannot simply take Dean and Sam as their vessels and complete the plan on their own. They need the Brothers Winchester to make the conscious and willing choice to play those roles. And considering how much pressure each side continues to put on Sam and Dean to make that choice, there is a very real danger (from the angelic and demonic point of view) that they won't get what they want.
So while Michael kills Anna and puts the brothers back where they belong so that the timeline proceeds as he understands it must, all his explanations to Dean are not simple confidence. It's also a calculated effort to convince Dean that the choice is meaningless, because in truth, that choice is where the power lies. Right now, in this story, Sam and Dean are the most powerful beings in the world, because their choices define the course of history.
Which is why I am still convinced that God's true plan is not what Michael thinks it is, and why the previous discussion of finding God is still relevant. Anna was wrong to lump that mission in with the use of the Colt. The Colt was always a longshot; it wasn't designed to kill angels. More importantly, the brothers tried to use the Colt and it failed. That tactic was already disproven.
Finding God and going over the heads of Michael and Lucifer, and perhaps discovering the true plan (of which, necessarily, fooling Michael, the angels, and the demons into thinking they were right would be a part) has yet to be disqualified. In fact, because it was brought up and continues to be dismissed as impossible by the antagonists makes it all the more likely to factor into the story on one level or another. This kind of foreshadowing feels very much like what the writers did to prepare for Sam's eventual fall.
I'm still confident that this is gong to default to one of the basic differences between humans and angels in many traditions: that humans have the gift of free will. Sam and Dean have a choice, or Michael and Lucifer wouldn't be trying so hard to convince them otherwise. And when that's the ultimate conclusion one is meant to draw from an episode where characters are constantly saying they have no choice, it's just a sign of how strong an episode it was.