I found a more legit way to fix the problem for now. I am running Mountain Lion, so I wouldn't try this unless you're also on Lion/Mountain Lion. (It should work for Lion, since the Java release/package I used is for Lion/ML.)Option 1 (tested by me, I would recommend):
Download JavaForOSX2013-002.dmg, which I found here:http://supportdownload.apple.com/downlo ... 13-002.dmg
or a mirror I made here:http://bayfiles.com/file/OUfH/gkJu5R/Ja ... 13-002.dmg
You can verify the checksum from the official Apple lists if you're paranoid, here:http://lists.apple.com/archives/securit ... 00000.html
One problem though, when you try to install it, it says a newer version is installed.
So to get around this, I used a nifty piece of software for the Mac called Pacifist; it lets you do various things with installer packages.
Get it here:http://www.charlessoft.com/
After you install Pacifist, open it up.
Mount the JavaForOSX2013-002.dmg DMG and drag the JavaForOSX.pkg into the main Pacifist window.
In the new Pacifist window that opens up, select the top item in the list, "Contents of JavaForOSX.pkg".
Then click the "Install" item in the window...
During the install, it asks whether you want to merge, replace, or skip files... I chose to "Replace" any files it asked about (and you can check the box so it doesn't ask again for every file). This may take ~2-5 mins.Option 2 (untested, but I think it will work):
For those of you that want a slightly easier way that doesn't require third party software, you can try this. YMMV, as I haven't tested this.
I extracted the contents of the main installer in the JavaForOSX2013-002.dmg with Pacifist. There are 4 sub-packages.
I uploaded the .zip here:http://bayfiles.com/file/OUOH/ufCLK4/Ja ... ckages.zip
Just extract and install each package that was in the .zip. Order doesn't matter.
The main goal here is to bypass the version check, which I think is a function of the aggregate installer.
Now when I run: "$ java -version" in Terminal I get 1.6.0_43! Previously I had 1.6.0_45 after installing the "Java for OS X 2013-003" Apple update.
PMS 1.80.0 works for me now, and I'm pretty sure this will be the least hacky and least apt to break future (re)updates to Java. Checking for system updates even shows "Java for OS X 2013-003" as installable again!
Hope this works for you all until PMS code can be fixed. If you have issues getting this to work, I'll try to check back here.