How to prevent Drush pm-update from backing up symbolic links?
This should probably be in the Drush issue queue. Maintainers can help you work through issues if you want to make a patch.  Be sure you are using the latest version of Drush.  By intention, it looks like Drush should only behave as you describe if the --dereference option is specified; without that, it should not follow and archive symlinks.  Run Drush with --simulate to see what actual tar commands, etc. Drush is running.  Post results and followup questions to the issue queue.