I think a common way of disabling peoples ability to create mystcraft worlds is to simply remove the book binder. That way people can make linking books for easy travel to and from eachothers houses and to mystcraft worlds that you create for them.
And if its just for you and your kid and friends, couldn't you just agree not to use quarries and the likes in overworld? Usually if you set them up with a flat desert world to mine in instead, people don't actually want to mine in overworld any more. Just make it a rule that no one ruins the landscape of overworld(unless they actually want to build something there). If you disable all the means that can be used to ruin the landscape, you will be disabling half the game making it very hard to build anything.