I believe that Drupal already prevents multiple users with the same name. So I added an override option that allows the peruserdir to create the directories by username rather than numbers.

In disknode.module, at function disknode_settings() around line 136 I added:

  $form['disknode_peruserdir_byusername'] = array(
    '#type' => 'checkbox',
    '#title' => t('Per-user directories override to directory by user name'),
    '#default_value' => variable_get('disknode_peruserdir_byusername', 0),
    '#description' => t('Overrides the number-based user directories. The base directory will be created per user with the following format: "[basedir]/[username]". For example: "mybase/someuser"for the user "someuser".  PER-USER DIRECTORIES MUST ALSO BE SELECTED!'),
  );

And in disknode.inc at function __disknode_getbasedir() I changed the function to look like this:

function __disknode_getbasedir()
{
  global $user;
  $basedir = variable_get('disknode_base', '');
  if ((intval(variable_get('disknode_peruserdir', 0)) == 1) && !user_access('escape user directory')) {
    if (intval(variable_get('disknode_peruserdir_byusername', 0)) == 1) {
      $basedir .= DIRECTORY_SEPARATOR.($user->name);
    }
    else {
      $userdir = preg_replace("#^.*(.)(.)$#", "\\1".DIRECTORY_SEPARATOR."\\2", "00".$user->uid);
      $basedir .= DIRECTORY_SEPARATOR.$userdir.DIRECTORY_SEPARATOR.($user->uid);
    }
  }
  return $basedir;
}