Yes, God, is referred to 'He' in the Bible, but was not most of the Bible written by men. So, I don't think God really told the writers to call Him, He. Just an assumption, maybe. And, yes, Jesus was a man---He was born of woman. He had a male body. So, if you are a Christian, you can agree that He was a man. Just as Adam and Eve were created with human bodies and therefore had gender. Doesn't necessarily mean their creator was Male or Female. Most men call their boats, 'she' and their trucks, 'she'. I've also noticed if a man calls a strange dog, he will say, "come here boy" until the dog corrects him if he's wrong.
Since this is a work of fiction, the reference to God as she seemed like the authurs chance to raise some eyebrows and promote discussion. I would say her plan worked. Although reading some of the other ideas of krishna seem a possibility too. Abigail does carry a Bible though that Arthur gave her. It will be interesting to see if this topic does develop in the next couple books of this series.