By default Drupal stores all configuration into database. Below example shows how to remove / delete configuration object of 'automated_cron.settings', i.e. remove cron settings :
<?php
// Using \Drupal::configFactory()
\Drupal::configFactory()->getEditable('automated_cron.settings')->delete();
// Or \Drupal::service.
\Drupal::service('config.factory')->getEditable('automated_cron.settings')->delete();
?>
// Using \Drupal::configFactory()
\Drupal::configFactory()->getEditable('automated_cron.settings')->delete();
// Or \Drupal::service.
\Drupal::service('config.factory')->getEditable('automated_cron.settings')->delete();
?>