<p>Specifically, we've got some external JavaScript tracking code on our sites that throws itself into an infinite loop each time an anchor is clicked on.</p>

<p>We don't maintain the tracking code, so we don't know exactly how it works.  Since the code causes the browser to lock up almost immediately, I was wondering if there's anyway to log the results of Firebug's 'profile' functionality to an external file for review?</p>

Forget HTML and make a PDF. HTML printing is extremely variable - not just across browsers but across different versions of the same browser. PDF is a lot easier.
Even if you get it exactly right with one browser / font setup / printer / phase of the moon, it will be the most fragile thing you've ever had to maintain. No matter how long you think it will take to make a PDF (and it's not really that hard as there are some free libraries out there), HTML will ultimately take a lot more of your time. PDF readers are widely deployed and print more consistently than even Word files.