From what I understand, the Zodiac Zeta weapon wasn't destroyed or anything, it was just traded in for the Umbral and Astral Nodes... So it is still intact, but as a part of that one lady's collection somewhere... And you also get a replica of the weapon.

But in terms of the story doing it all, with a sentient weapon especially, is kind of cruel.
"I no longer need you, kthxbai, oh and I got this thing that looks like you."