Lee shared a writing credit on 2012's animated Wreck-It Ralph before writing Frozen and directing with Chris Buck. Since Frozen made about a kajillion dollars for Disney and promises to pump more millions into the studio bucket, she had her choice of projects, and A Wrinkle in Time was supposedly one of her favorite books as a child. Disney produced an adaptation of the book for television in 2003, but a decade has passed, which means no one in their target audience remembers that.
Admittedly, I have not seen Frozen, and I am not a child, nor a parent, but I did read A Wrinkle in Time as a child and found it to be a magical experience. I, too, imagined that my father was a scientist and disappeared and had to be found, which required journeys through magical worlds and such. Admittedly, it has been many years since my childhood, and, now that I think about it, I didn't actually read the book, but it was read to my class by our beloved teacher, and for some reason I missed the last day of class, and so I don't know how the book ends.
All of which means nothing, of course, to modern audiences. I saw Wreck-It Ralph and thoroughly enjoyed it, so if Lee can bring that kind of verve to a book from 1962, have at it. No word yet on whether she might direct the new version, which appears to be a live-action project.