<?php
$xml = <<< XHTML
<ul><br/>
<li></li><br/>
</ul>
XHTML;
$dom = new DOMDocument;
$dom->loadXml($xml);
$xp = new DOMXPath($dom);
$brElements = $xp->query('//ul/br');
while($brElements->length > 0) {
$brElements->item(0)->parentNode->removeChild($brElements->item(0));
}
echo $dom->saveXML($dom->documentElement);