To disable a default search filter, you will have to remove it from the list of enabled filters, for example, in the init method of a corresponding Studio plugin. Disabling the filter will also remove it from the filters in the library's search mode.

public class FooStudioPluginBase extends StudioPlugin {

  override
  public function init(editorContext:IEditorContext):void {
    super.init(editorContext);

    <!-- 'fooFilter' is the FILTER_ID of the added filter panel -->
    editorContext.getEnabledSearchFilterIds()
        .splice(editorContext.getEnabledSearchFilterIds()
        .indexOf("fooFilter"), 1);
  }
}

Warning

Please note, that you do not need to remove the filter via RemoveItemsPlugin. Removing the filter manually, could result in errors in the Studio.