Wether you use the WSASoap or WSSESoap class, you can set the following on your object:
$obj->signBody = false;
When calling the signSoapDoc method you can pass it the option signSpecificHeaders to limit it to only certain header elements
i.e
$options = array("signSpecificHeaders" => array(WSASoap::WSANS_2005 => array('Timestamp' => true)));
$objWSSE->signSoapDoc($objKey, $options);
If you need to use xmlseclibs and not wse-php then just look at the code in the signSoapDoc on what it is doing via xmlseclibs to do this