What would be the lesson or moral of a story where the villain takes in the young heroes to build an army against the government/god/higher power that tricked the youths into believing they were the chosen ones to defeat the villain
First off, it sounds like the story is portraying higher power as deceptive and manipulative, which I would call 'lower power,' since 'higher power' applies power for the good, not to exploit. So you could say one moral of the story is that higher power is actually negative/evil/low.
Second, it sounds like there is a anti-moral that opposes stories that motivate youths into defeating villain/villains/villainy.
So it basically sounds like this is an anti-story designed to defy traditional moral narratives where higher power is good and trustworthy and the reader is motivated to identify with some hero that struggles against villainy.
Basically it sounds like some literary analyst decided that traditional narrative patterns are too predictable or mundane, so s/he would try to write a story that defies them.
So maybe the moral of the story is that traditional narrative patterns/values are bad and subverting them with anti-morality is good.
You could make an argument that such anti-morality expresses the fundamental satanic value of opposing God and/or traditional goodness.