If the registry keys are in HKLM it would be possible to do in a package boot step, no?
Certainly it is possible, but doing so is not worth the effort needed to test the methdology when Group Policy is a much simpler and proven technology. Furthermore, you would actually have to deploy an update to a machine to disable the autoupdater. Isn't the desire to disable the autoupdater everywhere, universally and permanently? Group Policy is the correct technology to use for this purpose. Finally, if you have any systems that have application dependencies on older versions of JRE, then you'll have to modify and test multiple packages. (Already you'll have to modify and test three packages at a minimum: x86, x64, and x86-on-x64).
By the way, do you have any idea about how to efficiently turn off the new prompts in Java 7 which blocks access if the version is not the newest?
I don't know about any prompts in JRE7 that do this. There is a prompt on JRE6 systems that invokes the upgrade to JRE7. The fix here is to uninstall JRE7 / upgraded to JRE7.
If similar prompts have been added to JRE7 to get the latest updates, then it seems that the fix would be to either update the system, or disable the autoupdater (if it can't be updated).