Religious characters in her books usually seem to be viewed as positive or negative based on how narrow-minded they are about it. In Blood and Sand, Thomas's epiphany is along the lines of "well, whether Presbyterian or Muslim I'm worshipping God, do the details really matter?" And there's a strong contrast drawn between the fairly easy-going Ottomans he joins and the Wahhabi fundamentalists they fight.

She did do a few in the 16th century! The Queen Elizabeth Story, The Armourer's House, Brother Dusty-Feet, Lady in Waiting (and three short stories in We Lived in Drumfyvie, if one can find it.) But the first three are cosy children's books and the fourth about Raleigh, and I don't remember religion as much of an issue in any of them.

There's some interesting material in Adonis. It's worth a read.