Religion in Sci-Fi

Reading Xenocide by Orson Scott Card.  “The gods are naked, and we must clothe them.”

In this part of the story Qing-jao, one of the godspoken, must discover the cause of the disappearance of the fleet.  She can find no reason, except that the gods did it.  But revealing that is a problem because only the godspoken are “allowed to see that they (the gods) are the cause of all that is and was and will be.”

Card has developed a system that merges scientific reality with religious belief.  Now, what does he do with it?