Module submission guideline - configuration storage
My advice to you is to submit your sandbox to Drupal.org Project Applications, and see what people say.  Its fairly rare to get an outright rejection.  People will inspect your code, offer suggestions for improvement, etc.  Better to get started ASAP.

As for your specific issue:  I think the way you are going about it is not in accordance with The Drupal Way ™.  Your best bet would probably be to generate a PHP file, only allowing your module to access this sort of administrative control from the site in Default.