What a neat question! As usual I don't have a definite answer, but the sources say "later known as Jeanne d'Arc," so my phrasing above was careless--I would guess that the name was applied when people, most likely related to the history of Doshisha and her husband, began to recount her history; there were a LOT of European books flooding into Japan once the Meiji era got started, late 19th-early 20th c., so they would have picked up knowledge of Joan of Arc then (a quick search suggests that there's a Schiller play about her, I mean Joan not Yae, which was first translated into Japanese in 1903). I would need to do more textual research than I can easily handle at this point to give you a good rundown on Japanese attitudes toward Joan at the time, but it's a fantastic question.