There isn't a simple way to click a button and detach your forked repository from the parent. You can either create a new repository that is not a fork or you can delete the repository and recreate it as an empty one and add whatever you like to it.
I would probably recommend:
Create a new repository with a new name
Set it up the way you want it including with your new scripts and the submodule configuration
Make sure it is all working the way you like
(Optional) Delete the forked repo
(Optional) Rename the new repository to the same name as the forked repo
