Yes, it can get confusing when tracing the religion thread. For example, when I started my search, I was very convinced that my M(a)cPhee family were Presbyterian. It ends up that my McPhees are actually Roman Catholic, but Little John married Margery MacMillan who was the one who raised all of the children in the Kirkhill Church . . . though they all were baptized in the Catholic church too--just for insurance???
Earlier I think it was you who said that Scottish ties were stronger than religious ones, and that is what Donald Simon Fraser told me too about ten years ago. Donald Simon has now passed but he was one of the main historians for Glengarry.