Can you create a script to programatically run update.php on multiple drupal sites
I've written a similar script on a 50+ site multisite install. You want to use the command line powertool drush for this, and then run the command 

drush updb


from a shell script, ex:

cd /var/www/site1-environment/
drush updb --uri=http://site1.com 
cd /var/www/site2-environment/
drush updb --uri=http://site2.com 
... etc


Of course if all of these sites are in the same multi-site structure than you won't need to repeat the cd command in your shell script.