They saint in the necklace is a member of Vatican that died stopping a dungeon break when the black haired best friends grandma was younger. They posthumously sanctified her and she is one of the people they honor on sacrifice day or whatever it was called which was just a holiday to celebrate and remember the lives of people who had died sacrificing themselves to stop dungeon breaks. The reason she didnt come out of the necklace for so long was because it needed a certain amount of divine energy and with the original creator God being gone there isn't a lot of people woth strong divine energy anymore.
Im glad theyre finally addressing Agnes take on all this though since she was a strong believer in the order of strict and good and they really dont appreciate non-believers and MC has just been running around actively following a different god all together that Agnes is seeing give gifts and favor to MC
Bro is it just me? I thought that Saint in the necklace would become the God of their world considering that she is one of the 5 heroes mentioned that killed the corrupted ML. Plus she's giving the "holy" aura, and there's no way she'd be stucked in a necklace for that long waiting for a saint worthy of the title