<?php

$xml = <<< XHTML
<ul><br/>
<li></li><br/>
</ul>
XHTML;

$dom = new DOMDocument;
$dom->loadXml($xml);
$brElements = $dom->getElementsByTagName('br');
while($brElements->length > 0) {
    $brElements->item(0)->parentNode->removeChild($brElements->item(0));
}
echo $dom->saveXML($dom->documentElement);

<ul>
<li/>
</ul>