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();
?>

Reference: