Well, I usually hear the biblical Mary and Joseph referred to as "Mary and Joseph," but I usually say my kids' names in their birth order, so if yours were mine I would always say "Joseph and Mary." That wouldn't so much make me think of the Mary and Joseph. Do you ever call your Joseph "Joe"?
Are you set on the name Mary, or would a variation on it be just as pretty to you but lessen the weirdness you're feeling -- like Marianne, or Miriam, or Mary ___ (Jane, Sue, Eve, -- oh, Marieve is a pretty name that works well in English)? I was at a baby name site recently that gave similar names, or names that had parts of your chosen name in it, etc. Like this.
Are you set on the name Mary, or would a variation on it be just as pretty to you but lessen the weirdness you're feeling -- like Marianne, or Miriam, or Mary ___ (Jane, Sue, Eve, -- oh, Marieve is a pretty name that works well in English)? I was at a baby name site recently that gave similar names, or names that had parts of your chosen name in it, etc. Like this.