$sku = '12345';
$storeId = 2;
$metaTitle = 'Updated meta title';
$id = Mage::getSingleton('catalog/product')->getIdBySku($sku);
if ($id) {
     Mage::getSingleton('catalog/product_action')->updateAttributes(
         array($id),
         array('meta_title' => $metaTitle),
         $storeId
     );
}

sku  _store  meta_title
sku1         Default meta title
     store 1 Store 1 meta title
sku2         Default meta title
     store 2 Store 2 meta title