<?xml version="1.0" encoding="utf-8"?>
<childrens>
<child id="1" name="klassa">
<item id="1">Sasha</item>
<item id="2">kosta</item>
<item id="3">Petya</item>
</child>
<child id="2" name="klassb">
<item id="4">Vasya</item>
<item id="5">Kolya</item>
<item id="6">Alesha</item>
</child>
</childrens>

<?php 
$dom = new DOMDocument; 
$dom->load('klass.xml');
$doc = $dom->documentElement;
$list = $doc->getElementsByTagName('child');

foreach ($list as $element) {
         if ($element->getAttribute('id') == '2') {
             $doc->removeChild($element);
         }
}
$dom->save('test1.xml'); 
?>

<?php 
$dom = new DOMDocument; 
$dom->load('auto.xml');
$xpath = new DOMXPath($dom); 

$squery = $xpath->query('/childrens/child/item[@id="6"]'); 
$el = $squery->item(0);
print_r($el);
//$domRef->parentNode->removeChild($el);
$dom->save('test1.xml'); 
?>

<?php 
$dom = new DOMDocument; 
$dom->load('auto.xml');
$xpath = new DOMXPath($dom); 

$squery = $xpath->query('/childrens/child/item[@id="6"]'); 
$el = $squery->item(1);
$el->parentNode->removeChild($el);
$dom->save('test1.xml'); 
?>