Then I'm sure it won't be the first 'religious' book to do so.
As I said, it doesn't stop it being relevant - if the themes are about truth, kindness etc. If it says kill non-believers, it is arguably not about "goodness", only self-serving.
If I were following a religion and found out it was total fiction and that the gods were merely aliens, I wouldn't be following the good parts of the book. I'd abandon the entire thing in search of GOD himself. A moral code would be irrelevant without God as it's source, because it will vary from man to man.