I wasn't able to do it entirely with array_column, but this works ... as long as the product and item arrays have the same number of elements.

<?php
$oriArr = array(
   2 => array(
      'A' => 'Mapping item1',
      'B' => array(1 => 'product1', 2 => 'product2', 3 => 'product3'),
      'C'=>array(1 => 'item1', 2 => 'item2', 3 => 'item3')
    ),
   3 => array(
      'A' => 'Mapping item2',
      'B' => array(1 => 'product4', 2 => 'product5', 3 => 'product6'),
      'C'=>array(1 => 'item4', 2 => 'item5', 3 => 'item6')
    )
 );

$keys = array_column($oriArr,'A');
$products = array_column($oriArr,'B','A');
$items = array_column($oriArr,'C','A');

$result = [];
foreach ($keys as $k) {
        $result[$k] = [];
        if (isset($products[$k])) {
                $i = 1;
                foreach ($products[$k] as $p) {
                        $result[$k][] = [$products[$k][$i],$items[$k][$i]];
                        $i++;
                }
        }
}

var_dump($keys,$products,$items);
var_dump($result);

I think the bigger issue is you lose the keys

Original Code

array (
  0 => 
  array (
    0 => '1138',
    1 => '6500722',
  ),
  1 => 
  array (
    0 => '1144',
    1 => '6501046',
  ),
  2 => 
  array (
    0 => '113',
    1 => '6294915',
 );

You can use a simple foreach instead of the second array_map:

function colsFromArray(array $array, $keys)
{
    if (!is_array($keys)) $keys = [$keys];
    return array_map(function ($el) use ($keys) {
        $o = [];
        foreach($keys as $key){
            //  if(isset($el[$key]))$o[$key] = $el[$key]; //you can do it this way if you don't want to set a default for missing keys.
            $o[$key] = isset($el[$key])?$el[$key]:false;
        }
        return $o;
    }, $array);
}

Output

array (
  0 => 
  array (
    'product_id' => '1138',
    'product_sku' => '6500722',
  ),
  1 => 
  array (
    'product_id' => '1144',
    'product_sku' => '6501046',
  ),
  2 => 
  array (
    'product_id' => '113',
    'product_sku' => '6294915',
  ),
)

Sandbox

the problem is that it seems too laggy, since it iterates twice over this.

There is no real way to not iterate over it 2 times, but you probably don't want to throw away the keys either.

That said you can recursively unset the items you don't want.

function colsFromArray(array &$array, $keys)
{
    if (!is_array($keys)) $keys = [$keys];
    foreach ($array as $key => &$value) {
        if (is_array($value)) {
            colsFromArray($value, $keys); //recursive
        }else if(!in_array($key, $keys)){
           unset($array[$key]); 
        }
    }
}

colsFromArray($array, array("product_id", "product_sku"));
var_export($array);

Same output as before

This is easier to do by reference. Rather or not that is faster you'll have to test the 2 and see.

Sandbox

As a final note you shouldn't assume the key will exist or that keys will be an array unless you type cast it as an array.

You could also do it with array filter

function colsFromArray(array $array, $keys)
{
    if (!is_array($keys)) $keys = [$keys];
    $filter = function($k) use ($keys){
       return in_array($k,$keys);
    };
    return array_map(function ($el) use ($keys,$filter) {
        return array_filter($el, $filter, ARRAY_FILTER_USE_KEY );
    }, $array);
}

There is some small performance benefit to declaring the function for filtering outside of the loop (array_map).

Sandbox

Since the DB result is row-based (usually), every column will have some value (even if it's NULL). So unless you mess with the result somehow, you should be safe. I do practically the same in some of my code.