Look, I'm not saying it was Miriam for sure but...you know what? Fuck it. It was Miriam. She came up with the Ted story on the spot while giving MC shark eyes and deciding if she could get away with killing him. It's obvious that she is taking sexual advantage of the mentally challenged gardener from his "I put seeds in Miriam" comment, as well as when she talks about him being "extremely good with his hands" while not-so-subtly fondling herself. I don't doubt for a second that the church is somehow involved in researching anomalies for their own purposes and would require a person who is apparently devout and could provide access to any part of the convent at any time for any reason (such as abducting young nuns). Miriam comes off as hypocritical enough to spew holier-than-thou rhetoric while being involved in an illicit affair with an individual who is physically an adult but has the mental capacity of a five-year-old. But to the rest of the the nuns she would just be the doddering cook who takes care of the retard groundskeeper and locks the doors at night.
But hey, that's just my conjecture and, admittedly, doesn't take into account the totality of the physical evidence (ice block=puddle of water mixed with victim's blood, dent in the hardwood).