JRE 7u67 -- assistance with trusting sites and setting security

I use a script to add sites to the exception list.

#!/bin/bash

exceptionList="$HOME/Library/Application Support/Oracle/Java/Deployment/security/exception.sites"
exceptionListPath="$HOME/Library/Application Support/Oracle/Java/Deployment/security/"
SITES=( "http://Site1" "SITE2" "SITE5" "https://SITE4" )

MYLOG="$HOME/Library/Logs/java_exception.log"

if [ ! -d "$exceptionListPath" ]
then
mkdir -p "$exceptionListPath"
/bin/echo "Created exception list path in: $exceptionListPath " >> "$MYLOG"
fi

touch "$exceptionList"
touch "$MYLOG"

/bin/echo "=================Start `date "+DATE: %m-%d-%Y TIME: %H:%M:%S"`===================" >> "$MYLOG"
for MYSITE in "${SITES[@]}"
do
if grep -Fxq "$MYSITE" "$exceptionList"
then
/bin/echo "NOT ADDED:  $MYSITE - Already exists." >> "$MYLOG"
else
echo "$MYSITE" >> "$exceptionList"
/bin/echo "ADDED:  $MYSITE" >> "$MYLOG"
fi
done

/bin/echo "=================Complete `date "+DATE: %m-%d-%Y TIME: %H:%M:%S"`===================" >> "$MYLOG"


#Scott Code to modify ownership of ~/Library/Application Support/Oracle
echo "Modifying permissions"

USER="$(w | grep console | awk '{print $1}')"
echo "current user is: ${USER}"

echo "Modifying /Users/${USER}/Library/Application Support/Oracle"
/usr/sbin/chown -R ${USER} /Users/${USER}/Library/Application Support/Oracle

exit 0

Since the site stuff is user level, this script gets the logged in user and then adds the sites to their exception list.

I know I poached this from somewhere. I am pretty sure it was Rich Trouton, but I am sorry I can't remember where I got it.

Sounds like you're successfully getting Java settings configured, so I'd say the java blocked dialog is due to your safari settings. You'll need to set Safari to trust the Java plugin for that page. This is handled in the safari.plist, and strangely enough I randomly had to write a script to do this myself this morning.
Here's what I came up with:

#!/bin/bash

#path to user's Safari plist
declare -x CONSOLE_USER="$(who | awk '/console/{print $1}')"
declare -x loggedInUser="$CONSOLE_USER"
theFile=/Users/$loggedInUser/Library/Preferences/com.apple.Safari.plist

# kill safari if it's still running
while [[ `ps aux | grep "Safari" | grep -v grep | awk 'NR<=1 {print $2}'` != "" ]]; do
    kill `ps aux | grep "Safari" | grep -v grep | awk 'NR<=1 {print $2}'`
done

# kill cfprefsd in case it's protecting the plist.
killall cfprefsd


##############
#Configure the Safari JAVA Plug-In settings
##############

#Determine how many DICT items exist in plist
DICT_COUNT=`/usr/libexec/plistbuddy -c "print ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies" $theFile | grep "Dict" | wc -l | tr -d " "`
#Determine if a entry already exists for whatever you're looking for
YOUR_THING_PRESENT=`/usr/libexec/plistbuddy -c "print ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies" $theFile | grep "foo" | wc -l | tr -d " "`


if [ $DICT_COUNT -gt 0 ] && [ $YOUR_THING_PRESENT -gt 0 ]; then
    #Both DICT exists and our entry exists. Set the preferences
    for idx in `seq 0 $((DICT_COUNT - 1))`
    do
        val=`/usr/libexec/PlistBuddy -c "Print ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${idx}:PlugInHostname" $theFile`
        if [ "$val" == "foo" ]; then
            /usr/libexec/plistbuddy -c "set ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${idx}:PlugInHostname foo.com" $theFile
            /usr/libexec/plistbuddy -c "set ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${idx}:PlugInLastVisitedDate $(date)" $theFile
            /usr/libexec/plistbuddy -c "set ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${idx}:PlugInPageURL https://foo.com/" $theFile
            /usr/libexec/plistbuddy -c "set ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${idx}:PlugInPolicy PlugInPolicyAllowNoSecurityRestrictions" $theFile
            /usr/libexec/plistbuddy -c "set ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${idx}:PlugInRunUnsandboxed  True" $theFile
        fi
    done
elif [ $DICT_COUNT -gt 0 ] && [ $YOUR_THING_PRESENT -eq 0 ]; then
    #Java array has DICT entries, but our thing is not one of them. Add it to the next available array index
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies array" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${DICT_COUNT}:PlugInHostname string foo.com" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${DICT_COUNT}:PlugInLastVisitedDate date $(date)" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${DICT_COUNT}:PlugInPageURL string https://foo.com/" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${DICT_COUNT}:PlugInPolicy string PlugInPolicyAllowNoSecurityRestrictions" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:${DICT_COUNT}:PlugInRunUnsandboxed bool True" $theFile
else
    #No DICT entries exist. Create new one at index 0
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies array" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:0:PlugInHostname string foo.com" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:0:PlugInLastVisitedDate date $(date)" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:0:PlugInPageURL string https://foo.com/" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:0:PlugInPolicy string PlugInPolicyAllowNoSecurityRestrictions" $theFile
    /usr/libexec/plistbuddy -c "add ManagedPlugInPolicies:com.oracle.java.JavaAppletPlugin:PlugInHostnamePolicies:0:PlugInRunUnsandboxed bool True" $theFile
fi
defaults read $theFile

I haven't had time to switch this over to Python to deal with cfprefsd properly, so this is just bash and it kills cfprefsd. Tested on 10.10, 10.9, 10.8, and 10.7 (even though 10.7 Safari doesn't have per-site settings I wanted to see if writing the dict to safari's plist would freak it out at all and it did not) but make sure to test, test, test yourself.

Bones of this script came from another script I found on jamfnation back in the day, too, but I'm not sure who originally posted this.

Thanks nkalister! I'll preface my reply in saying I am no scripting guru -- when I run the script I receive the "terminated 15" in Terminal, signifying processes are killed, but there doesn't seem to be much behavior changed in Safari. To be clear I am checking a particular website in my safe sites list. I am also checking the Safari Preferences > Security > (Internet Plug-Ins) Website Settings.

Anyway, I still receive a "Java Blocked for this website" message... any more thoughts of what I might be missing?