He was an much of an enigma then as now! Perhaps there was a child who was somehow denied treatment or asylum in the CChurch and the story evolved into the death, not only of the child, but also of the wife? Might explain her departure before the end of their mission to South America and his solitary existence for the rest of his life. Perhaps she blamed him for the child's death - perhaps he was somehow responsible for it in her eyes. Possibly the event was so traumatic that she never spoke of it again and he was forever alone.
Then again, perhaps there was no child at all. But whatever happened, I'd bet my life on the Catholic Church being somehow involved. He was a fanatic about the Church.