One really interesting thing about the church scene is just how Aziraphale reacts when Crowley shows up, especially when compared to the Bastille scene.
I mean, look at his face when he hears Crowley's voice in France.
He just lights up. Whether you believe he arranged his own arrest with this outcome in mind, or whether you think it was just a lucky coincidence that Crowley happened to be nearby, Aziraphale is clearly thrilled that he's there.
That is the face of an angel who's just learned that his immediate future no longer involves his own beheading.
And he doesn't even hint. We don't get any of the puppydog eyes he uses to get Crowley to make Hamlet popular or clean the paint off his coat. He's totally relaxed and at ease during their conversation, he agrees that he's lucky Crowley was in the area, and then Crowley frees him. He doesn't have to ask. By this point in their relationship, they've clearly reached the stage where the idea that Crowley might not be totally willing to save an angel from discorporation doesn't even occur to either of them.
And now compare it to Aziraphale's reaction when Crowley shows up to save him in the Blitz.
It's basically the same situation. Aziraphale has got himself into a situation where he's about to be murdered by humans (and for some reason can't just miracle the problem away) when Crowley shows up to save him.
Except this time, Aziraphale isn't thrilled. If anything, he sounds rather annoyed. "What are you doing here?" His first assumption is that Crowley must be working with the Nazis, for god's sake, even though he knows that that isn't Crowley's style, and was genuinely shocked a few centuries earlier when he thought that Crowley was admitting to being responsible for the French Revolution. (Crowley is right to be offended.)
But of course, it's easier for Aziraphale to believe that Crowley is somehow involved with the Nazis, because there has to be some reason why he's in that church. At this point, Aziraphale honestly finds it easier to believe that Crowley could be working with Nazis than that, after their big argument, Crowley could still be working to protect him.
After all, how familiar do we think Aziraphale is with the concept of forgiveness?
Given the Fall, given the Flood, given humanity's exile from the Garden.
Given the whole Heaven and Hell set up that he and Crowley's jobs revolve around, which really depends on the idea that humans cannot repent after death. Aziraphale might be able to redeem some of the humans on Earth, but once they've died, if Crowley's convinced them to commit whatever magical number of sins you have to commit to warrant eternal damnation, then that's it.
Given the fact that Aziraphale's own 6,000 years spent living on Earth might well be meant as a punishment for letting the serpent into Eden, because despite its reputation on Earth, Heaven really isn't as big on the whole 'love and forgiveness' thing as everyone seems to think.
Aziraphale lives in a universe where if you mess up, even if you didn't mean it, even if you regret it right after, then that's it. So why wouldn't he apply that to his friendship with Crowley?
Why would it occur to him that you could fall out with somebody and then make up afterwards with no hard feelings? That you could say things, hurtful things, that you didn't mean— because you were scared and because he wanted holy water and because it was too much and too fast— that you could fall out so badly that you don't speak to each other for nearly a century and that, after it all, they'd still walk across consecrated ground and bomb a church for you. And even save your books in the aftermath.
And Crowley, it's worth mentioning, doesn't even seem to realise this. Crowley is baffled and a little insulted that Aziraphale would even ask why he was there. Obviously he's keeping his angel out of trouble— isn't that basically his second job by this point? He's totally casual about offering Aziraphale a lift home, though I suspect that that might be a conscious decision to deliberately act like everything's back to normal, so as to signal to Aziraphale that everything is indeed back to normal. Crowley (and we get to see this trait more later on when it comes to the whole Alpha Centauri thing) forgives so easily that he doesn't even notice he's doing it.
And that, I think, is why this is such an important moment in their relationship.
It's not just the rescue of the books that makes Aziraphale realise the true depth of his feelings about Crowley. It's the fact that, in his own way, Aziraphale considers himself to be just as unforgiveable as Crowley, and Crowley forgave him regardless.