I get scared when I see documentation* telling you that you must do something or live data might be lost. It's far to easy to miss that documentation and suddenly you've potentially lost the only copy you have of certain files.

How about writing a settings file to the container that would get checked before certain operations (in decreasing order of importance):
* Adding or editing new container
* Deleting files
* Any write

The settings file would contain something to uniquely identify the Drupal installation. This might be the domain name of the site (although that doesn't necessarily protect dev VMs) or some random data generated when adding the first container.

(*second paragraph of "Containers" at http://drupal.org/project/storage_api )