To answer your question, while PHP is not listed among the supported documents on Google's list:
http://www.google.com/webmasters/facts.html (see last fact), it is definitely supported and I don't see any types of penalties being imposed for it. The best example to compare this is to go to
http://www.php.net
The whole site is powered on PHP and both its results in the SERP's and its PR show that php is fully supported.
WG