I agree,
Magdalene (I prefer
Magdalena) and
Raphael do have strong Catholic vibes for me (but then I am Catholic and love both names).
But, I think the question is what are you going to raise your children as,
Baptist or Catholic (or neither)? I mean with a Catholic father I don't see the problem with the names, especially if you like them.
On the other hand to me,
Miriam and
Jonas (
Jonah more so) have a Jewish vibe.
I love
Nathaniel!