$parent_mc_id  = 15; //id родителя
$relarr = []; //конечный одномерный массив
$ctr =  Array //входной многомерный массив
    (
        [0] => stdClass Object
            (
                [mc_id] => 4
                [rel_id] => 2,3
                [ctr] => stdClass Object
                    (
                        [0] => stdClass Object
                            (
                                [mc_id] => 6
                                [rel_id] => 2,3
                            )

                        [1] => stdClass Object
                            (
                                [mc_id] => 2
                                [rel_id] => 1,2
                            )

                        [2] => stdClass Object
                            (
                                [mc_id] => 6
                                [rel_id] => 2,3
                            )

                        [3] => stdClass Object
                            (
                                [mc_id] => 2
                                [rel_id] => 1,2
                            )

                    )

            )

        [1] => stdClass Object
            (
                [mc_id] => 6
                [rel_id] => 1
                [ctr] => stdClass Object
                    (
                    )

            )

    );

parseArray ($mc_id, $ctr, $relarr);
function parseArray ($mc_id, $ctr, $relarr){
    foreach($ctr as $key => $ctr_object){
        $c_mc_id = $ctr_object->mc_id;//id дочернего элемента
        $rel_arr = explode(',',$ctr_object->rel_id);
        $relation = [];
        foreach($rel_arr as $key => $rel_id){
            $relation['mrt_id'] = $rel_id;
            $relation['mr_agent'] = $mc_id;
            $relation['mr_contragent'] = $c_mc_id;
            $relation['mr_status'] = 1;
            array_push($relarr, $relation);
        }
        $subctr = (array)$ctr_object->ctr;//пытась унать уесть ли внук
        foreach($subctr as $subctr_obj){
            if(!empty($subctr_obj)){
                parseAgent($c_mc_id, $subctr_obj, $relarr);//если есть то снова вызываем эту функцию
            }
        }
    }
    return $relarr;
}

$subctr = (array)$ctr_object->ctr;//пытась унать уесть ли внук
foreach($subctr as $subctr_obj){
    if(!empty($subctr_obj)){
        parseAgent($c_mc_id, $subctr_obj, $relarr);//если есть то снова вызываем эту функцию
    }
}

(
    [0] => Array
        (
            [mrt_id] => 2
            [mr_agent] => 1
            [mr_contragent] => 4
            [mr_status] => 1
        )

    [1] => Array
        (
            [mrt_id] => 3
            [mr_agent] => 1
            [mr_contragent] => 4
            [mr_status] => 1
        )

    [2] => Array
        (
            [mrt_id] => 1
            [mr_agent] => 1
            [mr_contragent] => 6
            [mr_status] => 1
        )

)