That was how those stories worked: the issue is raised and vehemently dismissed; the episode explores the issue thematically; Sam and Dean find a way to talk about the issue.
Man, how I miss those days. The writers once excelled at this kind of character driven standalone episodes.

That means we should be due for at least one highly dramatic Amelia-centric episode at the end of the season.
You're quite possibly right. Even if it is not a pregnant Amelia, there are just too many ways that the return of the character can go terribly wrong. I even speculate that Sam might be forced to sacrifice Amelia in order to complete the trials; I am not sure if the current set of writers would see any problems with such a turn in the story. Overall, I can think of no scenario where she returns that I would even remotely appreciate.

It feels like that should have been a slow, difficult recovery.
Yeah, this is the second time that Dean's potentially interesting storyline is simply brushed under the carpet. The first time was his post-hell arc, but compared to his (post-)purgatory storyline, Dean's S4 arc was basically a masterful exploration of his hell-related issues. Where did the concept of consistent character exploration go this season?

And it was a particularly odd thing for Dean to say, given that he has always been adamant that it will never be over.
Yeah, it's kind ironic, isn't it? I mean, on the one hand the writers frequently look back to S1 for characterisation - like Dean's 'no chick flick moments' from the Pilot - but on the other hand they cannot even remember the most basic character moments from S1, like his convinction in Shadow that there will always be something to hunt. /sigh