You didn't read the quote. He's saying that it's when an author doesn't try to insert a moral message that his true morals shine through. That has nothing to do with writing messed-up stories, because then you are intentionally using morals you may not agree with, just for fun. Neither does it have anything to do with imagination.
It's a sort-of counter-argument to your "Ender's Game seems targeted at a young-adult audience, so I doubt it's filled with deeper meaning.", because it's when exactly when you are not inserting deeper meaning that your true beliefs shine through, which is why it's perfectly reasonable to deconstruct the morality of the book.