The file management aspect is easily managed by applying permissions using the Admin, File Manager. The FCK browser will respect this. Remove view permissions from the root and give view and write permissions to your desired subfolder.

Removing the button can be done if you hack the file Providers/HtmlEditorProviders/Fck/FCKeditor/editor/dialog/fck_link.html

Put something like this around the div holding the button at line 63:

<% If DotNetNuke.Security.PortalSecurity.IsInRoles("PortalSettings.AdministratorRoleName") Then%>

button code

<%End If%>

You'll have to repeat this when you upgrade, or if the next version already has this option, as Locopon has mentioned, then you can drop it altogether.

Rob