Here's an easy fix proposal for improving (and simplifying) Confluence's printing a lot: create a new style sheet for just printing purposes. I've used one on a number of occasions and with a print-only stylesheet it's possibly for you to entirely lose the custom jsp code for the "printer friendly" page since you could just set the style sheet to hide the navigation when printing. Could use the same technique for the PDF generation?

At the moment the printed pages have unnecessary "back to previous page "links and form elements which aren't necessary at all.

If you're unfamiliar with the technique, read for example the following:

http://webdesign.about.com/cs/css/a/aa042103a.htm