You forget that Meteion was at the edge of the universe. The Ancients could'nt have killed her even if they tried, nor even then be able to manipulate and counter the gathered dynamis in Ultima Thule to their advantage. The Ancients were focused on rebuilding their world than wanting to fight despair.
Even then if we're going to start nitpicking the story like this, then we might as well go ALL the way back to every single thing in this story to nitpick some of the power inconsistencies if this is truly such a bother. Why is a single WoL more powerful than another set of WoLs? How come Nidhogg took his sweet time to ravage Ishgard unless if we're treating him like Meteion....maybe he wasnt trying hard enough? How come the Garleans with all their superior magitek still lost the war? What about Emet-Selch whom lived multiple lives and for thousand of years suddenly thought "oh I wonder if maybe I try to understand these people and follow them". Its stuff like this when you start dissecting a simple jrpg story causes more unnecessary crutches and issues that would make the average story cynic have an aneurysm.