wanderingchana-
It’s not bubbe maises. I don’t know the exact makor but when I was in a history class my teacher (a brilliant man, and a rav as well) said that it comes from Rabbeinu Gershon who supposedly sat shiva when his son converted to Christianity, though there’s a question about a girsa with the story. It is well known however that R’ Shlomo Eiger sat shiva when his son R’ Leibel became a chosid (I think of the Kotzker). While I’m not suggesting we learn from that, and as the story goes R’ Akiva Eiger, R’ Shlomo’s father, disagreed with him, you certainly see the concept of sitting shiva when someone converts out of the religion. I don’t know what the source for sitting shiva for intermarriage is though.