Can't you just try to replace the body content with the document.body handler?
if your page is this:
<html>
<body>
blablabla
<script type="text/javascript">
document.body.innerHTML="hi!";
</script>
</body>
</html>
Just use the document.body to replace the body.
This works for me. All the content of the BODY tag is replaced by the innerHTML you specify. If you need to even change the html tag and all childs you should check out which tags of the 'document.' are capable of doing so.
An example with javascript scripting inside it:
<html>
<body>
blablabla
<script type="text/javascript">
var changeme = "<button onClick=\"document.bgColor = \'#000000\'\">click</button>";
document.body.innerHTML=changeme;
</script>
</body>
This way you can do javascript scripting inside the new content. Don't forget to escape all double and single quotes though, or it won't work. escaping in javascript can be done by traversing your code and putting a backslash in front of all singe and double quotes.
Bare in mind that server side scripting like php doesn't work this way. Since PHP is server-side scripting it has to be processed before a page is loaded. Javascript is a language which works on client-side and thus can not activate the re-processing of php code.