I meant that you're putting too much emphasis on the religious symbolism. The events that occur are an analog that religion posited as supernatural, when in fact they are wholly natural. How those events are labeled is not that important, except that they reflect the overall theme, which is psychological isolation, and its value to human survival and greatness.
You native to Moscow? Your country was the heart of the bloodiest experiment in psychological 'togetherness' the world ever witnessed. It was also the most fanatically religious country in the Occident, prior to enslaving and mass murdering itself. Considering that most of the world has never learned from the slaughterhouse created by communist ideology, the fact that Hideki Anno was able to crucify the idea so thoroughly should hold a lot more weight.