Deploy with disabled auto-update:

1. open the msi in Orca
2. click on "tranform"
3. select "new transform"
4. go to the "property" table
5. edit the entry as followed: AUTOUPDATECHECK=0
6. edit the entry as followed: JAVAUPDATE=0
7. edit the entry as followed: JU=0
8. click on "transform"
9. click on "generate transform"
10. save the transform (mst).

This is what I did for the latest version of Java Version 7 Update 40:

On Success

1.  Run the batch file "Remove Old Version of Java" with params "".

2.  Run the batch file "Wait" with params "".

3.  Launch "$(KACE_DEPENDENCY_DIR)\jre-7u40-windows-x64.exe" with params "/s /v /norestart AUTOUPDATECHECK=0 JAVAUPDATE=0 JU=0"

This worked for both 64bit and 32bit versions of Java.  You just have to change out the file.

After installing Java 7 Update 40 the item shows as a newly installed program. While I am not aware of any switches to remove this from showing up initially in the Start Menu, I added this line in my batch after the install to remove the shortcuts out of the folder. This should hide any trace from the normal user that anything was installed on the system:

del /f /q "c:\programdata\Microsoft\Windows\start menu\Programs\Java"

Another way to delete the shortcuts from the Start menu.

Create a custom action and paste this script in it.

dim strProgramData, strJavaPath

set wshShell = CreateObject("WScript.shell")
set scrFilesystem = CreateObject("Scripting.FileSystemObject")

strProgramData = wshShell.ExpandEnvironmentStrings("%ProgramData%")
strJavaPath = strProgramData & "\Microsoft\Windows\Start Menu\Programs\Java"

if scrFileSystem.FolderExists(strJavaPath) then
 scrFileSystem.DeleteFolder(strJavaPath)
end if