You have to strip the script tags from your HTML string.
var p = new DOMParser(),
doc = p.parseFromString("<html><body>...</body></html>", "text/xml");
$('script', doc).remove();
This works with Firefox/Chrome, although I don't know about other browsers. Note this will only work with well-formed (x)html.
EDIT: If you also want the JS, you can amend the previous code thus:
var scripts = [];
$('script', doc).remove().each(function() {
scripts.push($(this).html());
});
Mind you, you don't even have to remove the script tags. Now that the response is in its separate DOM document, it will not mess up your own scripts, and you can access whatever content you need from it using easy $('selector', doc) jQuery.