While I am not an 'expert' in child psychology or child education or religion (or anything, really!), I decided to offer my (humble) opinion in an effort to at least try to encourage the individual somehow.
It seems that science and religion (or spirituality) don't mix very readily. I'm not sure exactly why, but that's how it is. Not in every case, but surely most of the time. Scientific evidence often 'disproves' or otherwise brings into question, certain religious (though not necessarily spiritual) claims and even some beliefs. How DO you explain these things?