Administration was done via a client application rather than a web interface. Normally, you'd right-click on a site's icon in a list view and choose "Connect to...", then do what work you need to do, then right-click on the site icon and choose "Disconnect from site".
The only problem was that, in a misguided attempt at logical arrangement, the context menu was ordered alphabetically. That meant "Delete site" was located just before "Disconnect from site".
Fortunately, there was an "are you sure?" confirmation dialog that came up first.
Unfortunately, they used almost-identical confirmation dialogs for both "delete" and "disconnect"...
Yes, indeed, I did once kill a production website.