The development of increasingly complex cerebral functioning will inevitably lead to an intrinsic human moral equilibrium. It is an inalienable part of our nature to question traditions, constructs and current standards. Of course, questioning and experimentation go hand in hand and so some error is to be expected, but we are now at a point in our history where the wealth of recorded knowledge from those who questioned before us has enabled us to form ever more complete pictures; society is continually progressive, and the more we know about our world and ourselves, the more information we have available to make our society a more symbiotic one.
If kids are rejecting religion, I suspect that it is more to do with a desire to discover the truth for themselves - not to be coerced and forced into predefined moulds - than it is to do with them being inherently amoral or immoral. I think the quest for truth authenticated through experience is vital to any person's progress and to chastise kids with a view to denying them that experience not only suppresses their thirst for edification and clarity but also stunts wider human development. Not to mention it is highly hypocritical since all people of faith question and many who now have faith had cause to take it up. Expecting someone to believe something they've never had cause to believe, while simultaneously denying them the experimentation that invokes cause, is actually just a recipe for enforced, superficial faith. It's psychological despotism.
I say give people the tools to search not only the world but themselves, impart them with the wisdom to make their own decisions and when they make mistakes recognize that error is an intrinsic part of human nature.