I found out that php >=5.3 has garbage collector cleaner. So, when I import chunk of articles I call gc_collect_cycles(); to clear memory out of all entities which script will needs no more. The script is slowing down no more!
If you are using a framework, check if it has its own cache system. If you are using doctrine turn off SQL logger
/** @var $em EntityManager */
$em = $this->getContainer()->get('doctrine')->getEntityManager();
$em->getConnection()->getConfiguration()->setSQLLogger(null);
and then clear doctrine cache after every chunk is imported
$em->clear();