Try this then:
SELECT conversation_id, COUNT(*) c
FROM xf_conversation_recipient
GROUP BY conversation_id HAVING c > 1;
and in your case:
$value1 = $this->_getDb()->fetchCol("
SELECT conversation_id, COUNT(*) c
FROM xf_conversation_recipient
WHERE user_id IN ('4465','1')
GROUP BY conversation_id HAVING c > 1
");