/srv/example.com/www/public/magento/js/, instead of their web accessible path, e.g.
StackOverflow saves my life again.
Update: (08:52am, 18/03/10) - As Avi Shefi notes, I didn’t actually find a solution to the problem. Avi has updated the StackOverflow question with the following:
media/jsdirectory belongs to the same user as the Magento folder
dev/js/merge_files flag to 0 in the database before doing this and then reverting).