Oh hiya bang...
Well, it's extremely complicated to write stories for children, many good authors of adult books have tried it and given up!
I think you have to have just one main moral, or theme, in a children's book. Religious themes can be tackled without resorting to obvious characters. Remember C.S.Lewis' 'The Lion, the Witch and the Wardrobe'? One of the main characters was Aslan, a lion that represented Jesus. Lewis was a Christian and he saw no problem in creating fictitious characters to represent Christian ideas.
Not all characters in a story need to have an exact parallel to the WBTS! Keep the main idea simple but add depth to your characters! Let the children know what they are like, explicitly or implicitly.
Main ideas/themes could include:
Beware anyone who says only he knows the truth.
Letting other people control what you think can be dangerous.
How people can be persuaded to do bad things by being in a group - the bad things can be made to look good. (disfellowshipping?)
Such ideas cannot be argued against and should not trigger JW mind-alarms, when their children read the story.
Adult JWs are too arrogant to recognise their own hypocrisy, but children aren't, so a good children's story may sow the seeds for future reevaluation of their beliefs when they are asked to conform to parameters they know in their heart to be wrong.
If you don't want to get too real (witchcraft) why not create a completely fictitious fantasy world inhabited by Tolkeinesque type creatures? Should be fairly safe. You can then call the characters anything you like, it's how they tell the moral that counts.
Of course this is all just MHO! Hope this helps and doesn't just make you give up!