I think the sub-factioning of the gnome faction should play a major part in this, and resolves a lot of the mechanical problems being cited. Sure, your players may have diplomacy mods of 30+, and be able to sense motive there way out of pretty much any lie. However, that doesn't mean that the gnomes the party talked to weren't intending to do as they said. It just means that another group of gnomes either overruled or overpowered them (or simply neglected to consult them at all). Some of the gnomes very well ought to be allied with the party, and should the party meet up with the gnomish ship again (hopefully in the near future, so the event is still fresh), then many of the gnomes ought to side with the party, or at least remain neutral in the fight.
That would actually make a great set piece. The party chases the ship down (or teleports to it, which would certainly speed things up), and finds the gnomes on the verge of violence about what to do with the McGuffin, and the left behind PC's. I'm not sure how you'd be able to accomplish this without a bit of railroading, but you might consider a well timed Scry informing the party of this split within the gnome faction. That would add a lot to the final encounter between the gnomes and the PC's, especially if the PC's can't tell which faction the gnomes belong to at first, and have to judge quickly before things get out of hand (who wants to kill the gnomes who've been trying to help all along).
As to the feeling that the adventure was "done", and that the removal of the McGuffin is simply stealing the party's thunder, I must disagree. If the party obviously had at least one challenge left ahead of them (removing the artifact from the city), then there should be no reason for them to assume that the quest was pretty much in the bag. Such an assumption seems almost arrogant on behalf of the PC's, because they're essentially stating that they've done enough work on such an epic quest, and so they're giving up caring about finishing it. I suppose it's time to reference LOTR again: Did Frodo and Sam give up when they reached Mordor, and Frodo was paralyzed? They certainly had done quite enough to get there, so they ought to not have to face any more challenges before they finished the quest. It's an oversimplification, but I feel the gist of the idea still applies: the PC's are getting lazy at the end of the quest, and so you shouldn't pull any punches in keeping up the challenges because of that.
My hat is off to you regarding your improvisational skills. You managed to impliment a major plot twist that doesn't really conflict with anything in your campaign (as I understand it), and did it nearly subconciously. An aside: Should it really matter whether a DM plans things or not? As a player, how are you supposed to know the difference (if you have a compitent DM), and so how should it matter?
I'm not sure about the merit of Geas as a motivation for the plot. Could you expand on how the Geas was placed, and why the PC's accepted it? I think that would clear up a lot of misconceptions about it.