It should be noted that there is yet another update for Java available from Software Update. This one disables the java browser plugin by default; also, if you manually re-enable it and go a while without using it, the plugin will again be automatically disabled. This behavior is probably Safari-specific.
It's my understanding that there is a followup update to Java as well.
Run Software Update (Apple menu > Software Update) to update Java.
Read this article that shows how you can tell if you are infected by reading default values from the Terminal. That's a read-only detection using the command-line terminal you already have on your computer: