Massachusetts Bay Transportation Authority officials have decided they will not take over direct management of the commuter rail when their contract with the Massachusetts Bay Commuter Railroad Co. expires next year. Since 2003, the MBTA has outsourced management of the commuter rail system to the MBCR, a private company. That contract ends in June 2013. Jonathan R. Davis, the MBTA’s chief financial officer and acting general manager, announced at the agency’s general meeting this week that the often-discussed idea of the MBTA taking direct control of the commuter rail will not be in the cards.