This script will add two servers to the Oracle Java Exception Site List. If the servers are already in the whitelist, it will note that in the log, then exit.Since these settings are stored on a per-user basis, I recommend running this script with a launchagent. That will allow the script to run with the logged-in user’s privileges and permissions.

gistfile1.sh

#!/bin/sh

# This script will add two servers to the Oracle Java Exception Site List. 
# If the servers are already in the whitelist, it will note that in the log, then exit.
# More servers can be added as needed. The existing server entries can also be set to be
# empty (i.e. SERVER2='') as the script will do a check to see if either SERVER value
# is set to be null.

# Server1's address
SERVER1='http://server.name.here'

# Server2's address
SERVER2='https://server.name.here'

LOGGER="/usr/bin/logger"
WHITELIST=$HOME"/Library/Application Support/Oracle/Java/Deployment/security/exception.sites"
SERVER1_WHITELIST_CHECK=`cat $HOME"/Library/Application Support/Oracle/Java/Deployment/security/exception.sites" | grep $SERVER1`
SERVER2_WHITELIST_CHECK=`cat $HOME"/Library/Application Support/Oracle/Java/Deployment/security/exception.sites" | grep $SERVER2`

JAVA_PLUGIN=`/usr/bin/defaults read "/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Info" CFBundleIdentifier`

if [[ ${JAVA_PLUGIN} != 'com.oracle.java.JavaAppletPlugin' ]]; then
   ${LOGGER} "Oracle Java browser plug-in not installed"
   exit 0
fi

if [[ ${JAVA_PLUGIN} = 'com.oracle.java.JavaAppletPlugin' ]]; then
 ${LOGGER} "Oracle Java browser plug-in is installed. Checking for Exception Site List."
 if [[ ! -f "$WHITELIST" ]]; then
   ${LOGGER} "Oracle Java Exception Site List not found. Creating Exception Site List."

   # Create exception.sites file
   touch  "$WHITELIST"

   # Add needed server(s) to exception.sites file
   if [[ -n ${SERVER1} ]]; then 
     /bin/echo "$SERVER1" >> "$WHITELIST"
   fi
   if [[ -n ${SERVER2} ]]; then
     /bin/echo "$SERVER2" >> "$WHITELIST"
   fi
   exit 0
 fi

 if [[ -f "$WHITELIST" ]]; then
   ${LOGGER} "Oracle Java Exception Site List Found."

  if [[ -n ${SERVER1_WHITELIST_CHECK} ]]; then

    # Server1 settings are present
	${LOGGER} "${SERVER1_WHITELIST_CHECK} is part of the Oracle Java Exception Site List. Nothing to do here."
    else	    
	# Add Server1 to exception.sites file
    if [[ -n ${SERVER1} ]]; then 
      /bin/echo "$SERVER1" >> "$WHITELIST"
      ${LOGGER} "$SERVER1 has been added to the Oracle Java Exception Site List."
    fi
  fi
  if [[ -n ${SERVER2_WHITELIST_CHECK} ]]; then

    # Server2 settings are present
	${LOGGER} "${SERVER2_WHITELIST_CHECK} is part of the Oracle Java Exception Site List. Nothing to do here."
    else	    
	# Add Server2 to exception.sites file
    if [[ -n ${SERVER2} ]]; then 
      /bin/echo "$SERVER2" >> "$WHITELIST"
      ${LOGGER} "$SERVER2 has been added to the Oracle Java Exception Site List."
    fi  
   fi
 fi
fi
exit 0

I made a few modifications to the file to run it as the current user from Casper or Casper Self Service without needing the launchAgent.

#Get Session User
currentUser=$(ls -l /dev/console | awk '{print $3}')

# Server1's address
SERVER1='http://server.address.com'

# Server2's address
SERVER2='server.address.com'

# Server3's address
SERVER3='server.address.com'

LOGGER="/usr/bin/logger"
WHITELIST="/Users/$currentUser/Library/Application Support/Oracle/Java/Deployment/security/exception.sites"
SERVER1_WHITELIST_CHECK=`cat "/Users/$currentUser/Library/Application Support/Oracle/Java/Deployment/security/exception.sites" | grep $SERVER1`
SERVER2_WHITELIST_CHECK=`cat "/Users/$currentUser/Library/Application Support/Oracle/Java/Deployment/security/exception.sites" | grep $SERVER2`
SERVER3_WHITELIST_CHECK=`cat "/Users/$currentUser/Library/Application Support/Oracle/Java/Deployment/security/exception.sites" | grep $SERVER3`