At that age she might be interested in Terry Pratchett's Discworld. The Discworld books are fun fantasy stories that don't overtly push an agenda, but have a consistent, subtle theme of mocking the absurd aspects of things like superstition and religion.
As a youngster they got me thinking about things more critically.
Examples of quotes in the books: "What have I always believed? That on the whole, and by and large, if a man lived properly, not according to what any priests said, but according to what seemed decent and honest inside, then it would, at the end, more or less, turn out all right" - Small Gods
"The presence of those seeking the truth is infinitely to be preferred to the presence of those who think they’ve found it." – Monstrous Regiment
"Goodness is about what you do. Not who you pray to." - Snuff
There are a lot of books. They are all stand-alone stories, but have continuity with recurring characters. Some are in more closely linked arcs, like the Death series, the city guard books and the witches books.
The Tiffany Aching series might not be a bad starting point. While they were among the last to be written, they introduce a young trainee witch who's power is basically being rational (much like other Discworld witches).