K.A. Applegate who wrote Animorphs was an atheist. I just realized the slug-like aliens called yerks who take over your mind (and turn turn you into a slave/a drone to the youth group cult called “the sharing”) could be taken as a metaphor for religion. Though maybe it is a stretch and she was more influenced by Invasion of the Body snatched , classic sci-fi horror and sci-fi.
I wish she had stuffed the book with more secular themes, but I don’t know if her publisher for young adults would have allowed it. (I haven’t read her other series, Everworld, but it deals with mythology in a parallel world where the gods continue ancient petty struggles at the expense of humans.)