There are two things I think I should point out here:
1. You don't need to uninstall Java 6 to be able to install Java 7. They will install side by side.
2. Protect currently does not offer the option to uninstall Java from target systems so you would need to manually uninstall Java 6 if you want it removed.
I hope this helps!
That makes sense in the fact that Protect is not a software deployment tool, but a patch management tool. I guess I have my answer.
I was coming at this problem from the view point of I install Java 6 when I image a machine, then Protect patches it throughout it's lifetime. It seems that Java 7 is as much a patch as it is the next version.