I needed to do this for a project recently and ended up with an extension to DOMElement: http://www.keyvan.net/2010/07/javascript-like-innerhtml-access-in-php/
Here's an example showing how it's used:
registerNodeClass('DOMElement', 'JSLikeHTMLElement');
$doc->loadHTML('');
$elem = $doc->getElementsByTagName('div')->item(0);
// print innerHTML
echo $elem->innerHTML; // prints 'Para 1
Para 2
'
// set innerHTML
$elem->innerHTML = 'FF';
// print document (with our changes)
echo $doc->saveXML();
?>