Like somebody else stated, having an omnipotent being on the side of the protagonists doesn't make for a very good plot device.
The whole point of the lightning Bolt in the Jesus scene wasn't to protect the guardian, rather it was to burn the symbols on the key into the hand of the guardian. It's all symbolic, it's about the eternal struggle between good and evil, resistance against temptation, and man choosing to do the 'right' thing.
In God's eyes man has to prove himself worthy before he can enter the gates of heaven and be rewarded with eternal life. If God intervened and gave man a helping hand, people would never get the chance to prove their worthiness. I guess you could say it symbolises the 'choice' between either castrating your self, or giving into temptation and being condemned to hell. It's the illusion of free will to make God seem benevolent.
At the end of the day, like the Bible and other stories involving 'God', it's fiction. It's writers choose the plot devices that convey the storyline best (in their minds). The very idea of 'God' himself is contradictory, so any story about him is inevitably going to be full of plot holes, contradictions, and fruitless ideals.
On the other hand, you could say if God only manifests himself through natural effects (such as lightning), then perhaps he was powerless to intervene as, for most of the film, they were inside the house or underground. But given that in the mind of his believers God is omnipotent and omnipresent, that in itself is a contradiction.
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