If anyone else finds resolution to this problem here:
I’m aware Semiologic’s frame buster plugin was updated some time ago to deal with this problem (I can’t say about any other frame buster plugins), so that would be worth a look.
And for those who do this manually, here’s what I use in my <head> element:
<?php if(strpos($_SERVER['HTTP_REFERER'], get_bloginfo('wpurl')) === false) : ?>
<script type="text/javascript">
<!--
if (top.location != location)
top.location.href = document.location.href;
//-->
</script>
<?php endif; ?>
The PHP if
checks whether the refer comes from your site or not. If it doesn’t the javascript frame buster code is added.