I work with a school district with over 20,000 students and 14,000 systems. New state requirements are affecting all school districts in Texas to fend off security exploits within Java 6; we were forced to push out Java Update 7 over Java 6. This caused an array of issues destroying legacy support for crucial local systems. We actually had to create a secure remote apps server harbouring the old version of Java just so staff could use the interal system to run reports.

This will not fix the issue but for those whom struggled to deal with old versions of Java; If you want to CLEAN ALL JAVA VERSIONS and then run a fresh installation with one version alone - the following commands in command prompt (or pushed via sccm/whatever) will be all that you need:

TO UNINSTALL ALL JAVA VERSIONS 1-7 (Silently)
wmic product where "name like 'Java%'" call uninstall /nointeractive

TO UNINSTALL ALL JAVA 7 VERSIONS (Silently)
wmic product where "name like 'Java 7%%'" call uninstall /nointeractive

TO UNINSTALL ALL JAVA 6 VERSIONS (Silently)
wmic product where "name like 'Java(TM) 6%%'" call uninstall /nointeractive

Java: SCCM 2012 Detection Methods
http://www.ronnipedersen.com/2013/03/java-sccm-2012-detection-methods/

Here's my messy fix that I've developed with the help of a few others regarding the "Your version of java is insecure" popups.  So far so good!

http://www.labareweb.com/java-1-7-auto-update-deployment-with-sccmmdt/

I deployed Java 7 Update 11 to clients to laptops, and if IE was opened, Java claimed to be installed but the files weren't all there.  The MSI exited with a 0 return code, and Windows' 'Add/Remove Programs' wizard said it was installed.  This left Java in an unusable state.  Reinstalling didn't fix it.  I had to uninstall what was there and then run a new install of Java. The uninstall wasn't silently working however.  One of the Java files (installer.DLL) didn't et installed, and the MSI generates an error if it's not there during uninstall.  You can click 'OK' and continue through the removal, but it's not fully automated.  In my chaining script, I had to install the 'Installer.DLL' file to the 'C:\program files\Java\jre7\bin' folder, execute the uninstall, and then install the fresh copy of Java.

Here is a way to deploy Java 7 Update 15 through a MSI and using LANDesk

First download Java from Internet Explorer at http://www.java.com/en/download/manual.jsp both the 32-bit and 64-bit

Run the .exe on your computer then go to the Users folder C:\Users\"username"\AppData\LocalLow\Sun\Java

Underneath you will fine two folders names  jre1.7.0_15 and jre1.7.0_15_x64. Inside these folders you will find a MSI and a Data1.cab. Move these to your server share or wherevere you store your packages and then open LANDesk and make your MSI package. Make sure that you incude the Data1.cab in the Additional files tab. 

Xonos, For Java version 5u22, I had to change the query to "name like 'J2SE%" for it to fire.

otherwise, this query is amazing! :)

http://docs.oracle.com/javase/7/docs/webnotes/install/windows/jre-installer-options.html#running

<jre>.exe [/s] [INSTALLDIR=<drive>:\<JRE_install_path>] [STATIC=1] [WEB_JAVA=0/1] [WEB_JAVA_SECURITY_LEVEL=VH/H/M/L]

<jre>.exe [/s] [INSTALLDIR=<drive>:\<JRE_install_path>] [STATIC=1] [WEB_JAVA=0/1] [WEB_JAVA_SECURITY_LEVEL=VH/H/M/L]

found on Java's support site.

http://docs.oracle.com/javase/7/docs/webnotes/install/windows/jre-installer-options.html#running

You can modify msi file registry) to disable auto updates and other settings
AUTOUPDATECHECK = 0
IEXPLORER = 1
JAVAUPDATE = 0
JU = 0
MODIFYREMOVE = remove
MOZILLA = 1
RebootYesNo = no