I had the same problem too. I have a Macbook Pro with OS X Lion. I too updated my mac with the 2012-006 update and it broke Java applets on Google Chrome.
After a lot of researching, I got to know that Chrome is a 32-bit browser and does not support the 64-bit Java 7 from Oracle and there was no way to run applets on Google Chrome on a mac until we get a 64-bit release of Chrome for the mac.
So, I went to the Mac App Store > Purchases tab and downloaded OS X Lion and installed it over my existing disk. Note that it seems like a big deal, but it went well for me and your data and settings do not get erased/reset. The old 32-bit Apple JRE 6 gets installed and until Google Chrome 64-bit is released, you can keep using it without problems as long as you don't reinstall the 2012-006 update.
It worked for me, so it should work for you too. I'm not sure if you have Lion or Mountain Lion, but I think the same trick should work for Mountain Lion too.
Did you try Settings -> Security -> Web Content ->Enable Java? – agirish – 2012-10-25T17:19:13.903