So, now the script just pauses to remind you to deactivate your plugins.  I tried to find a way to automate that, but have struck out so far.  If you know how, let me know!  I’ll give you credit.

Script follows:

#!/bin/bash

# Updated by: Jerry Bell
# License remains intact
# Changes:
# - Added a backup directory that is outside the document root. The previous script left copies of the database accessible
# - Added code to automatically determine the database name, database username, and database password from the wp-config.php file.

# - Removed "read" prompts - they're not really needed any more

# - Set tar to send the archive to the backup directory instead of document root.
#
# This program upgrades your existing WordPress installations that you are running on your server.
#
# You need to make the necessary adjustments to this script as needed for your situation.
#
# Make this script executable: 'chmod 777 wp_upgrade.sh'
# Run the script: './wp_upgrade.sh'
#
# Author: Aaron Toponce
# License: GPL v2
# Version: 0.1.2

# =================== Start of Script =================== #

# Provide the necessary directories to what WordPress installations need to be backed up space delimited
# Change as necessary and uncomment
# For example, if you had 3 sites in /var/www/site1, /var/www/site2 and /var/www/site3
# then it would look like below (do not add the trailing slash):
# directories=(/var/www/site1 /var/www/site2 /var/www/site3)
backupdir=/var/tmp
number=${#directories[@]}
# Testing that all directories specified above are valid before beginning
for (( i = 0 ; i < number ; i++ )); do
        if [[ ! -d ${directories[$i]} ]]; then
                echo "Directory ${$directories[$i]} does not exist."
                return 1
        fi
done

# First, we need to get the necessary file
cd ~

if [[ -f wordpress.tar.gz ]]; then
        echo "wordpress.tar.gz exists.  Please take notice to this upgrade before continuing."
        return 1
fi

wget -O latest.tar.gz http://wordpress.org/latest.tar.gz

echo "First disable all plugins on all installations before continuing."
echo "Press ENTER to continue..."
read blah

for (( i = 0 ; i < number ; i++ )); do
        clear
        cd ${directories[$i]}
        back_ts=$(date +%s)
        mkdir ${backupdir}/backup_${back_ts}
        echo "We are backing up the full directory, in case anything goes wrong. Press ENTER..."
        read blah
        tar -cvvf ${backupdir}/backup_${back_ts}/backup.tar ${directories[$i]}
        gzip  ${backupdir}/backup_${back_ts}/backup.tar

        # Timestamp in unix epoch format to create unique backup directories

        echo "backing up database for ${directories[$i]}:"
        # Backing up the necessary WordPress database
        wp_db=`grep DB_NAME ${directories[$i]}/wp-config.php | cut -f 4 -d "'"`
        wp_user=`grep DB_USER ${directories[$i]}/wp-config.php | cut -f 4 -d "'"`
        wp_pass=`grep DB_PASSWORD ${directories[$i]}/wp-config.php | cut -f 4 -d "'"`
        mysqldump --add-drop-table -u ${wp_user} -p${wp_pass} ${wp_db} > ${backupdir}/backup_${back_ts}/${wp_db}.sql
        # Make the necessary changes for what to backup.  This is the default as provided by WordPress.
        echo "Backing up the important files. Press ENTER..."
        read blah
        cp .htaccess wp-config.php ${backupdir}/backup_${back_ts}
        cp -r wp-content wp-images wp-includes/languages ${backupdir}/backup_${back_ts}

        # Time to copy the latest wordpress that we downloaded and overwrite all files
        echo "Getting the latest cp of wordpress. Press ENTER..."
        read blah
        cp ~/latest.tar.gz ./wordpress.tar.gz
        tar -zxvf wordpress.tar.gz

        # Overwrite all files
        echo "Overwriting all old WordPress files with the new."
        cd wordpress
        cp -rf * ../

        # Copy the files that we backed up back
        echo "Coping the important backed up files back in."

        cp -rf  ${backupdir}/backup_${back_ts}/.htaccess ${directories[$i]}
        cp -rf  ${backupdir}/backup_${back_ts}/wp-config.php ${directories[$i]}
        cp -rf  ${backupdir}/backup_${back_ts}/wp-content ${directories[$i]}/wp-content
        cp -rf  ${backupdir}/backup_${back_ts}/wp-images ${directories[$i]}/wp-images
        cp -rf  ${backupdir}/backup_${back_ts}/wp-includes/languages ${directories[$i]}/wp-includes/languages

        echo "Point your browser to the necessary site and run the upgrade script."
        echo "EG: http://example.com/wp-admin/upgrade.php"
        echo "Update your permalinks and .htaccess."
        echo "Install updated plugins and themes"
        echo "Reactivate plugins"
        echo "Press ENTER to continue..."
        read blah
done

clear
echo "Congratulations! You have successfully upgraded your WordPress."
echo "Please review that your browser resolves your site."
echo "Enjoy!"