The inquisition was right, we should have burn all Pagan, Heretics, witches and demons
Now being serious, the fact that there's only one adult being this nun, that they are in a desolate island, the place name is elysion, she never actually speak about God or have any symbols that could relate to Christianity or even buddhism and that she says that the island is a place where you can be free from prejudice and rejection, pretty much says that this is some kind of cult maybe derived from Christianity or a Pagan.
The fruits are our biggest clues about what kind of God she may be actually worshiping, maybe it's based around one from our world or specific created by this work, she could as well be just crazy though, however you can clearly see for her actions in the last part that she using both a emotional and physiological manipulation in the kids
My guess is that the younger brother will slowly get corrupted by the Nun and in the end the MC will have to fight against him