Not all the Ancients were sacrificed to Zodiark ("only" 75% of them) and the Ascians' desire was to return things to exactly how they were pre-Final Days. In order to do that they need to bring back all the Ancients who perished in the Final Days and their aftermath. Fully rejoining the reflections to the Source would not bring back Hermes, f'ex; he'd just be a fully rejoined Amon. You'd need to go another step to truly resurrect Hermes (kill Amon and transfer his soul to an Ancient's body, and somehow make his soul identify more with Hermes than Amon). Whether or not this would happen is uncertain, but.
Fresh new souls that aren't reincarnations of an Ancient could still be sacrificed to Zodiark for an Ancient's in return. That still wouldn't bring all of them back - the ones that died in the Final Days probably got sent to Meteion's nest, and the ones that were part of the second sacrifice to Zodiark may have simply sublimated into aether - but that's part of the tragedy of the Ascians: no matter how much death and destruction they cause, the world that was will never return.
The planet was pretty devastated before Zodiark was summoned; it's uncertain as to whether or not there was enough life left other than the Ancients to do something like summon Zodiark.
Fully rejoining a soul wouldn't return its vessel (body) to that of an Ancient, and as should be pretty apparent the Ascians do not have a high opinion of contemporary mortals. If a fully rejoined soul makes one equal to an Ancient, and the Ascians still planned on sacrificing these fully rejoined souls, it would become murder in their eyes (maybe) but they'd still find some way to rationalize it as "good" or "right." ("I'm improving your life by making you near-immune to disease and death by old age.") People will always find ways to justify their actions to themselves... unless they're a Saturday Morning Cartoon villain.