I agree with everything you said, but I recently saw the scene again on Facebook and Geordi explains to all of them that the saucer wasn't left behind because of the Prime Directive.
Out of universe I have been in discussion various times over the years about it and I cannot say that I KNEW they were going to have to retrieve it, but given what we know NOW, the senior staff of the ship all knew immediately and they were all in Starfleet for a long time after. They would have heard the news or perhaps even been in attendance when it was done.
It is possible that Picard would have thought it was a total loss, but wouldn't there have been news stories about the recovery that would've come up in their browsers that would've said it was retrieved largely intact? And do they all know there is a museum where NX-01, Enterprise-A, and the Bounty are all kept and wouldn't they have hoped that in some way their ship could get there?
Well, after some more thought, the retrieval effort takes place not long after the crash, given that it is going on when Spock arrives at Kirk's grave. In that time period there is a lot going on. Federation goes to war with the Klingons then almost immediately goes to war with the Dominion. The Breen attack Earth and Betazed is conquered. All this while the crew gets transferred to a new class of starship with the Enterprise E.
Also, the Fleet museum would have been something totally different at that point too, since the original Space Dock was still at Earth. The ships might have been there in those wire repair bay style docks, but the saucer section was pretty much scrap when they took it off world.