The following changes should be made via an existing transform - eg: sp1033.mst for English installs.
Action: PolicyFix Type: 3110 Source: (leave empty) Target: Set S = CreateObject("WScript.Shell"):X="HKLM\Software\JavaSoft\Java Update\Policy\":Y="REG_DWORD":S.RegWrite x&"EnableJavaUpdate",0,Y:S.RegWrite x&"EnableAutoUpdateCheck",0,Y:S.RegWrite x&"NotifyDownload",0,Y:S.RegWrite x&"NotifyInstall",0,Y:S.RegWrite x&"Frequency",0,Y:S.RegWrite x&"UpdateSchedule",0,Y
Action: PolicyFix Condition: NOT Installed Sequence - Just before InstallFinalize - eg: Sequence: 3183
I assume you mean the Windows directory on the workstation with Java installed, and not the common server.
It would be quite trivial to create these files using a bit of vbscript in a transform, to avoid having to deploy actual files.
with help from a post from Spartacus on AppDeploy.
Create two files, deployment.config:
deployment.system.config=file\:C\:/WINDOWS/Sun/Java/Deployment/deployment.properties
This can be a URL on a common server for enterprise wide settings. Create the deployment.properties file:
#deployment.properties #Sun Mar 13 17:58:03 GMT 2011 deployment.javaws.autodownload=NEVER deployment.javaws.autodownload.locked=
The "locked" line means that users can't override the setting in their own profiles.
Put these two files in a Sun\Java\Deployment subfolder of your WIndows Directory.
With 6u20 you could run:
msiexec /x {4A03706F-666A-4037-7777-5F2748764D10} /q
which would uninstall the seperate Auto updater but this seems to have been removed now.
Auto update appears to be the default, going into the Java applet in Control Panel > Advanced tab > JRE Auto download and selecting "Never Auto-Download" adds this line to Users\<username>\AppData\LocalLow\Sun\Java\Deployment\deployment.properties:
deployment.javaws.autodownload=NEVER
but I'm not sure how you could do this for all users.