Why not embed the code into your template.ascx/template.master instead?
For the XML Package try wrapping the script code with <![CDATA[]]>, result would look like:
Code:
<!-- Start of Woopra Code -->
<script type="text/javascript">
<![CDATA[
var woo_settings = {idle_timeout:'300000', domain:'mydomain.com'};
(function(){
var wsc = document.createElement('script');
wsc.src = document.location.protocol+'//static.woopra.com/js/woopra.js';
wsc.type = 'text/javascript';
wsc.async = true;
var ssc = document.getElementsByTagName('script')[0];
ssc.parentNode.insertBefore(wsc, ssc);
})();
]]>
</script>
<!-- End of Woopra Code -->