When you open a Site with Explorer view there are "Lists" and other folders and it is possible to delete this folders which causes problem for the site and it will be inaccessable. What can I do to make these folders (but document library folder) inaccessable? thanks
If they don't have access to delete these lists, then they cannot delete these lists. Even though in explorer view they might disappear, a refresh and they come back.
No an ideal scenario I know.
The only real alternative is to remove the functionality from the ribbon with HideCustomAction, you can do this by deploying a feature receiver with the code to hide it.