Perhaps our heroes will try to restore the shard with the Crystal, not knowing that it's not simply a matter returning it and that the Great Conjunction has to occur at the same time (and the urRus possibly needing to be there, too).
I don't know. I mean surely that would imply they were able to overcome the garthim, take the castle and hold the chrystal chamber, no? But then what? Did they just retreat and let the Skeksis back in. Surely they'd at least imprison, if not execute them in such a scenario.
I suspect that given where the shard was in the movie, that the healing of the crystal was one of the many paths Aughra had foreseen, so she kept it until the time was right.
As to how things end for the Heroes of Thra...I guess it depends at what point the story will leave off relative to the movie. It would be we weird to leave it on a high note with a new united Gelfling kingdom standing against the garthim, given how we know that ultimately ends. But I think it would be equally weird to end it on a total downer.
If I had to guess, I think the smart way to play this is to introduce a new twist in the story hitherto unsuspected. Like for example if the last act of the Resistance was to somehow hide a population of gelflings far away from the reach of the Skeksis. Escaped across the seas, or into down into some deep caves, or frozen in stasis somehow.
I have only a vague recollection of the sequel comics, but didn't that feature the Gelfling race back in full force just a few centuries later? Were they all decedents of Jen and Kira, or were those two not the last of their kind as they thought, just the last in that part of the Thra? Perhaps many, of not most are decended from those that returned from some diaspora.