DisallowedVirtualFolderNames setting is only used for multi site installations based on folder names, it has nothing to do with FCKeditor.
Currently I don't have the folders configurable as you would like. I do have a web.config setting RolesThatCanUploadAndBrowse that determines who can browse the server and upload files.
The logic for controlling what is seen in the browse dialog is in Web/Dialog/FileBrowseConnector.aspx.cs
You could potentially implement your own replacement for this and then just use the Web.config settings to point to your own version:
<add key="FileBrowserServiceRelativePath" value="/Dialog/FileBrowseConnector.aspx" />
<add key="ImageBrowserServiceRelativePath" value="/Dialog/FileBrowseConnector.aspx" />
<add key="LinkBrowserServiceRelativePath" value="/Dialog/LinkBrowseConnector.aspx" />
Hope it helps,