I was upset more that they kept trying to play it off like she was a morally grey character similar to Kiritsugu.
They manufactured that conflict with the woman who was against "murdering children" then threw that away when she admitted that she knew they were already dead. Yet Jeanne leans into it like she knows it's probably wrong or something.
Jeanne should have been a character with a similar conviction to Shirou's caliber, yet for faith rather than "saving everybody." Instead she was just super nice to everyone while saying "I'm not a holy maiden, even though the church totally anointed me one."
If they wanted to show maybe that there was some internal conflict for the girl she took over I could understand that, but it's not even a question in the series.