Just want to share this stuff with anyone there that might need it in the future. This is based from 4.5 code, not sure if it applies with 4.6
Delete a unmounted subsite instance does not work. You have to perform this first.
select application_group__delete(group_id) from application_groups where package_id = :your_subsite;
After that you can delete it by UI in the site map of unmounted application.
In case you have custom permissions to that subsite instance revoke those permissions first by UI or calling the db api.
