Use drush to clean up users with no roles (except authenticated user) assigned to them.

user_cancel_no_roles.php

#!/usr/bin/env drush
<?php
/**
 * This script removes all drupal users with no roles other than authenticated 
 * user assigned.
 *
 * This is useful in the case where a site's only users are admin or some 
 * other higher level role.
 *
 * Make sure to back up the database prior to running this as this cannot be 
 * undone.
 **/

$self = drush_sitealias_get_record('@self');
if (empty($self)) {
  drush_die("I can't bootstrap from the current location.", 0);
}

// we don't want to say yes each time.
drush_set_context('DRUSH_AFFIRMATIVE', TRUE);

$authenticated_user = array('authenticated user');
$users_deleted = 0;
$users_not_deleted = 0;

$result = db_query("SELECT uid,name FROM users WHERE uid > 1 ORDER BY uid DESC LIMIT 500");

foreach ($result as $user) {
  $uid = $user->uid;

  // make this runnable on d6 as well as d7
  if (drush_drupal_major_version() >= 7) {
    $user = user_load($uid);
  }
  else {
    $user = user_load(array('uid' => $uid));
  }

  // strip out the authenticated user
  $roles = array_diff(array_values($user->roles), $authenticated_user);

  // if there are no roles left, we should delete this user
  if (sizeof($roles) < 1) {

    $users_deleted++;
    // taken from the drush_user_cancel code
    // http://api.drush.org/api/drush/commands%21user%21user.drush.inc/function/drush_user_cancel/5.x
    if (drush_drupal_major_version() >= 7) {
      if (drush_get_option('delete-content')) {
        user_cancel(array(), $uid, 'user_cancel_delete');
      }
      else {
        user_cancel(array(), $uid, 'user_cancel_reassign');
      }
      // I got the following technique here: http://drupal.org/node/638712
      $batch = &batch_get();
      $batch['progressive'] = FALSE;
      batch_process();
    }
    else {
      user_delete(array(), $uid);
    }
  }
  else {
    $users_not_deleted++;
    drush_print("save: $user->name");
  }
}

drush_print("Total users deleted: " . $users_deleted);
drush_print("Total users NOT deleted: " . $users_not_deleted);