drush pm-update but leave an index file

We have set up some useful scripts that use drush and other command line functions to update several drupal sites on the same server using a single management site. When we drush pm-update drush will make a backup of the entire root directory of the site while it is working. It leaves behind the folder where it downloads Drupal and the sites folder. On our server this results in the directories and files being visible as there is no index file during this time (this is something we can fix but many servers might be configured this way). Also, because the owner of the files from drush updates is always root we need to chown the files/folders to the right account after drush is done. On a big update, however, this can take several minutes and during that time the site will be in 500 error mode (as the .htaccess file has the wrong ownership). We have overcome this issue with a custom 500 error page that shows a "This website is currently undergoing maintenance. It should back up within a few minutes. Thank you for your patience!" message so this is not as big of a deal.

What we'd like to be able to do is copy an index.html file in the site root and then run drush updates but have it leave the index.html file in the root so that we can display that same useful error message to our users "This website is currently undergoing maintenance. It should back up within a few minutes. Thank you for your patience!". After the drush updates are done we remove that file.

Is this possible? Like can we tell drush not to backup that index.html file when it updates Drupal? Or are we not doing the drush updates properly? Seems like they will always break a website while they are running.

Thanks!

-Drew