I'll also add the reverse of the question as that might be easier.

If I were to remove the group and holder item from the config file could I programmatically add them in the C# code later? 

Something like:

                var groupStart = new ToolControl("", new System.Web.UI.LiteralControl("<table class='CuteEditorGroupMenu' cellSpacing='0' cellPadding='0' border='0' style='float: right;'><tr><td class='CuteEditorGroupMenuCell'><nobr>"));
                var groupEnd = new ToolControl("", new System.Web.UI.LiteralControl("</nobr></td></tr></table>"));
                var index = editor.ToolControls.IndexOf(name);

                editor.ToolControls.Insert(index + 2, groupStart);
                // Add control here @ 
                editor.ToolControls.Insert(index + 4, groupEnd); 

The problem above is the new tool controls aren't set up correctly so it's not working.