Wrong angle?

With my first book, After the Dream, I started with the angle of tragedy and pain.  I started with my spiritual healing and insights and built a story around it.  I wasn't so much trying to tack a story on an agenda.  That kind of story is thin and preachy.  I was trying to show my own pain through metaphors, through the safe veneer of fiction.  The morals and meanings did not have to be tacked on.  They were at the core of the story.

Now, with my second novel, Pigs Fly, I have some spiritual content mixed in with a good story.  But I started with the characters and then the story, not the meaning.  Now, I'm going the reverse route and trying to weave meaning into a complete story.  The thing is I don't want the meaning to feel tacked on.  I want it to feel like an intrinsic piece of the story.

Now, there are thin stories that are merely a vessel, an excuse to preach.  That's what "The Last Mimsy," "Golden Compass," and "Pinocchio" appear to be to me.  The stories fall flat because they're more about the moral than they are about the story.  That, for me, is a problem.  However, there are so many stories that are all about story with little meaning or significance past the story.

I would like to hit a balance between the two, where I employ meaning in my story or employ story in my meanings.  I just fear that because I started with the story in this case and almost entirely left out the meaning until I have a first draft, any meaning I add will feel tacked on.  The whole reason I'm writing right now is to share meaning along with story, not just one or the other.  I guess I'll keep that in mind as I proceed with revision.