Modify instead of add a class in classes_array for theming purposes
Search for the key of the value you want to replace and then modify it. It's that simple.

function paddle_admin_preprocess_menu_block_wrapper(&amp;$variables) {
  if ($variables['delta'] === 'management_level_2') {
    // Search for the key
    $key = array_search('class_to_be_replaced', $variables['classes_array']);

    // If class was found, replace it
    if ($key !== FALSE) {
        $variables['classes_array'][$key] = 'class_that_replaces';
    }
  }
}