A multitude of aspects of the natural world that were considered miraculous only a few generations ago are now thoroughly understood in terms of physics and chemistry.
On the subject of the nature of the gods, the first question is Do the gods exist or do the not? It is difficult you may say to deny that they exist. I would agree if we were arguing the matter in a public assembly, but in a private discussion of this kind, it is perfectly easy to do so.
But in the end all religions point to the same light. In between the light and us, sometimes there are too many rules. The light is here and there are no rules to follow this light.
The religion that is afraid of science dishonors God and commits suicide. Every influx of atheism, of skepticism, is thus made useful as a mercury pill assaulting and removing a diseased religion, and making way for truth.