The function BuildPostQuery() in sitemap-builder.php needs a filter to modify the query when needed. For example when pages are only visible for logged in users or when certain meta values have been filled in
http://wordpress.org/extend/plugins/google-sitemap-generator/
Just played a little more with it and found some other issues.
XSLT should be loaded with set_url_scheme() so when the protocol is different the XSLT still get loaded. Setting this on $this->_url is a decision that need to be made. Maybe a filter on it would be nice so plugins can say some pages are different protocol then given.
Another issue is that XML and HTML files getting mixed up.