I missed this during all my travels, but the team at Intego posted a great overview:

Meanwhile, Apple also released Safari 6.0.4 for Mountain Lion and Lion, as well as Safari 5.1.9 for Snow Leopard. The new versions of Safari give users more granular control over which sites may run Java applets. If Java is enabled, the next time a site containing a Java applet is visited, the user will be asked whether or not to allow the applet to load, with buttons labeled Block and Allow:

Your options are always allow, always block, or prompt.

I still highly recommend disabling Java entirely in all browsers, but some of you will need it and this is a good option without having to muck with plugins.