Restrict IMCE directory access based on a taxonomy term value associated with workbench_access taxonomy access control. DIRECTORY_FIELD constant is a new text field on the term entity used for control.

custom_workbench.module

/**
 * Hijack IMCE Profile Loading to add a check for directory access coming from
 * a field on the access vocabulary term.
 *
 * @param $imce
 * @param $user
 */
function custom_workbench_imce_alter_profiles(&$imce, $user) {
  // Find access rules/terms for current user.
  $access_tree = workbench_access_get_user_tree($user);
  $tids = array();
  foreach ($access_tree as $tid => $access_item) {
    $tids[] = $tid;

    // If the user has access to the full list of available terms, don't
    // restrict the directories at all at this point.
    if ($tid == $access_item['access_type_id']) {
      return;
    }
  }

  // Provide default directory settings, just in case.
  $directory_base_settings = array(
    'subnav' => 1,
    'browse' => 1,
    'upload' => 1,
    'thumb' => 1,
    'delete' => 1,
    'resize' => 1,
    'crop' => 1,
    'mkdir' => 1,
    'rmdir' => 1,
    'rename' => 1,
    'rename_folder' => 1,
  );

  foreach ($imce['directories'] as $key => $directory) {
    if ($directory['name'] == BASE_DIRECTORY) {
      // Override default base settings if main directory has different config.
      $directory_base_settings = $directory;

      // Unset the main directory, since we're about to override if possible.
      unset($imce['directories'][$key]);
    }
  }

  // Load all terms for the user's tree.
  $terms = taxonomy_term_load_multiple($tids);

  // No terms loaded (no uploads access granted for this user), so bail.
  if (empty($terms)) {
    return;
  }

  // Assign any menus associated with terms that are accessible to the user.
  foreach ($terms as $term) {
    if (isset($term->{DIRECTORY_FIELD}[LANGUAGE_NONE])) {
      // Assign all associated directories to the IMCE Profile.
      foreach ($term->{DIRECTORY_FIELD}[LANGUAGE_NONE] as $directory_name) {
        $dir = trim($directory_name['value']);
        $directory_base_settings['name'] = BASE_DIRECTORY . '/' . $dir;
        $imce['directories'][] = $directory_base_settings;
      }
    }
  }
}