I did my rewatch. I have slightly more coherent thoughts now.
Here's the thing. I do think the ending makes sense in a way, because if we think about Crowley's character, he has always tried helping humanity. Most explicitly, I think the Edinburgh flashback builds on this, especially by showing he is punished for his actions to the extent where he ends up asking Aziraphale for Holy Water the next time they meet. It also shows the beginning of Aziraphale's discomfort with how the 'odds are stacked against humans' from the very beginning. So yes, I do think they were somewhat setting up for this kind of an ending.
HOWEVER, my issue is, there are too many plot holes in the finale. I know we had a time constraint with it, but there are so many basic questions which go unanswered. For example, if Michael destroys the Book of Life, how are Aziraphale and Crowley still there? How were they actually not the first ones to go, considering Michael probably was most upset with Metatron and Aziraphale? Next, how is the Bentley flying if Crowley is out of miracles? And also, why bother with the gangster plotline at all? It was underdeveloped and did not feel as satisfying or thematically logical as it should have. Again, I understand the time constraint, but perhaps that time would've been better utilised elsewhere.
Which brings me to the main problem. I think the entire fandom would have been satisfied with this ending, HAD Aziraphale and Crowley actually finally had a conversation. This finale felt like a repeat of the same dance they've been doing for ages. They did not really talk. I don't think Crowley had completely forgiven Aziraphale yet either, and how could he? There was no time. I wish they had just done away with some of the unnecessary plotlines, and focussed on the Book of Life and given Aziraphale and Crowley the time and space to sort through their feelings, go through their religious and philosophical dilemma and then make the choice.
Yes, it's their choice. Yes, it's a choice I think they would have made in every scenario. As much as it pains me. But why does that mean we could not have at least seen them happy together? Having a healthy conversation? Bidding farewell to them like they deserved to?
For a show that puts asking questions at its core, it has certainly left us with several unanswered ones.