When you delete a SCORM module, it's associated gradebook items (if any) will be orphaned. The user will then have no way to delete the items from the gradebook.
If you deselect the option to send grades to the gradebook for the module prior to deleting the module, it will remove the associated gradebook item(s). This behaviour should be applied when deleting a module directly. The attached patch introduces this behaviour when deleting a module.