A question

Why does Father McKinnon allow Hannibal Thurman to take custody of his children after Arthur's death? Given his emotional reaction to the twins at Mass (especially the one named Michael), I would think he would want to be a father to them after Arthur no longer can. I wonder why he would give them up to Thurman. Is it simply to protect Arthur's reputation? Or is McKinnon content just to have Eleanor in his paupers' graveyard?

I certainly hope it wasn't just an excuse in the frame story to get the confession out of McKinnon.