Mustafa,
We talk for this long time ago, and you say that this is hard to develop because kloxo can't know is there any other domain in this directory.
Can you make it with checkbox when delete domain/subdomain ?
For example, when you click delete it will show a checkbox with text: Do you want to remove and folder. Note*: If you have any other domains/subdomains in this directory, their files will be permanently deleted too. Or something similar.