Deferral for rebooting?

I think it might be better to check if updates require a restart before installing them. If the updates require a restart and there is a user logged in, you could prompt the user to make a choice:

1. Agree to the restart and install updates
2. Decline the restart and not install updates

This would also allow you to install updates that do not require a restart without bothering the user. It may require some tweaking depending on exactly what/when/how you want things to happen in your environment. You could install updates, then present the user with a jamfHelper with a timer. You could follow-up on systems after a certain point with a version of this script that does not give them an option to cancel/decline but instead just waits for them to acknowledge that a restart will occur once they click OK. Lots of possibilities.

#!/bin/bash

#---VARIABLES---------------------------------------------------------------------------

JAMFHELPER="/Library/Application Support/JAMF/bin/jamfHelper.app/Contents/MacOS/jamfHelper"
ICON="/System/Library/CoreServices/Software Update.app/Contents/Resources/SoftwareUpdate.icns"

#---FUNCTIONS---------------------------------------------------------------------------

#---------------------------------------------------------------
# getConsoleUsername
# Returns the current console user. An empty return means no one
# is logged in.
#---------------------------------------------------------------
getConsoleUsername()
{
/usr/bin/python -c 'from SystemConfiguration import SCDynamicStoreCopyConsoleUser
user = (SCDynamicStoreCopyConsoleUser(None, None, None) or [None])[0]
user = [user,""][user in [u"loginwindow", None, u""]]
print(user)'
}

#---------------------------------------------------------------
# promptRestartMessage
# Prompts user to acknowledge that a restart is required to
# finish installing software updates
#---------------------------------------------------------------
promptRestartMessage()
{
    local _window_type _title _heading _description _button1 _default_button

    _window_type="utility"
    _title="Apple Software Updates"
    _heading="Restart Required"
    _description="Your computer needs to install Apple software updates that require a restart to complete. Please save all work and click Restart."
    _button1="Restart"
    _button2="Cancel"
    _default_button="1"
    _cancel_button="2"

    echo "Prompting user to restart"
    "$JAMFHELPER" 
        -windowType "$_window_type" 
        -title "$_title" 
        -icon "$ICON" 
        -heading "$_heading" 
        -description "$_description" 
        -button1 "$_button1" 
        -button2 "$_button2" 
        -defaultButton "$_default_button" 
        -cancelButton "$_cancel_button"
}

#---------------------------------------------------------------
# displayRestartReminder
# Displays a persistent dialog as a reminder to the user that
# their system will be restarting to install updates soon
#---------------------------------------------------------------
displayRestartReminder()
{
    local _window_type _window_position _title _description

    _window_type="hud"
    _window_position="ur"
    _title="Restart Pending"
    _description="Apple software updates are being installed and your system will restart soon."

    echo "Displaying restart reminder"
    "$JAMFHELPER" 
        -windowType "$_window_type" 
        -windowPosition "$_window_position" 
        -lockHUD 
        -icon "$ICON" 
        -title "$_title" 
        -description "$_description" &
}

#---START SCRIPT------------------------------------------------------------------------

echo "Checking if a restart is required"

# Check if any updates require a restart to complete. The '[restart]' string exists on
# lines for updates that require a restart. The redirect 2>&1 is used to ensure all
# output from the softwareupdate command is sent the same way for the if evaluation
# because softwareupdate uses stderr for some reason for non errors (Don't ask me why).
# If no updates require a restart, all updates will install without user approval.
if [[ "$(/usr/sbin/softwareupdate --list 2>&1)" =~ '[restart]' ]]; then

    echo "Restart is required"

    # Check if a user is logged in to be able to accept or decline the restart.
    # If no user is logged in, the updates will install without user approval.
    if [ -n "$(getConsoleUsername)" ]; then

        echo "A user is logged in"

        # Prompt the user to accept the restart or cancel the updates
        if promptRestartMessage; then

            echo "User accepted restart"

            # Display a window reminding the user that a restart will occur soon
            displayRestartReminder

        # Exit clean if the user chose to not accept the restart
        else
            echo "User did not accept restart"
            exit 0
        fi

    # Log the fact that no user is logged in
    else
        echo "No one is logged in"
    fi

# Log the fact that no updates require a restart
else
    echo "No updates require a restart"
fi

# Install all updates with the --restart flag which will
# restart the system if any updates require a restart
/usr/sbin/softwareupdate --install --all --restart

exit 0