Makoto.
"But it goes against the theming of Persona 3!" you cry! But does it? In P3, we're told time and again that Death isn't necessarily the end, but a new beginning. Well, apparently, this is true to everyone but Makoto I guess, who gets to has his entire existence stopped by becoming a Seal to protect humanity, a worse fate than Shinjiro, the other party casualty in P3, had. If we're also talking about themes, it'd also be remiss to mention Messiah, his ultimate persona, and how it specifically mentions his "rebirth" as PART of the stories. So there.
Besides, I wouldn't necessarily mind it being a Nyarlathotep trick just to *really* hurt the SEES members more. We know this is what Elizabeth is going to be bulldozing for, and the road to hell IS paved with good intentions. So yeah, I'd also want it more for making Arena's story more interesting if it includes this idea. Part of me thinks this is going to be Sho's sole role though.