If I had to erase all the FFXIV NPCs from my computer and only my computer to bring back my loved ones, then yes, I would consider it.
If I had to erase all the FFXIV NPCs from everyone's computers, and indeed uninstall FFXIV from the world and remove it from existence, then no, I would not do it.
It's the difference between doing something that is a loss to myself and only myself, and doing something that is a loss to everyone.
Similarly, I would not, say, erase every single chicken or dog from the world just to bring back my loved ones. But that's what Emet-Selch is proposing, in that his plan would also kill the dragons, who are very much not Sundered souls.
EDIT: Also if the FFXIV NPCs suddenly appealed personally to me not to erase them, showing signs of sapience (or, to use a standard from Mass Effect's Mordin, the ability to perform advanced calculus as a species), then absolutely not would I sacrifice them to bring my loved ones back.
