IIRC, indexes aren't deleted by means of the indexes.conf changing. Instead, the indexes only stop being known by the indexer but the data itself is still on the filesystem. Have you verified that the folder structure is in fact deleted from the filesystem as well?
Deleting typically requires some account and capabilities that you can restrict. If someone goes on the filesystem directly and deletes the index's db folders then there's nothing you can do...just like anything else on the filesystem.
Hopefully that helps?