Disabling CKEditor in comments
Try

function MYMODULE_form_alter (&$form, &$form_state, $form_id)
{
  // comments
  // http://api.drupal.org/api/drupal/modules--comment--comment.module/function/comment_form/6

  if ($form['#id'] == 'comment-form') {
    $form['comment_filter']['format'] = array(); // nuke wysiwyg from comments
  }
}