An even simpler solution is to call delete_option( 'cron' ); once in some plugin. All automatically added cron jobs will get added again on the next visit/request of your site.
As a one case (mu) plugin that only runs whenever you activate it:
<?php
/** Plugin Name: Clean Cron */
register_activation_hook( __FILE__, function()
{
delete_option( 'cron' );
} );