What Apple has done with this update is to take the decision out of the user's hands--at least as it relates to Java. The OS will now monitor usage and simply disable Java if it is not used for an extended period of time. Other operating system platforms and software vendors may want to adopt a similar approach to automatically disable unused and unnecessary services to reduce exposure to attacks.
Kudos to Apple. It may be late to the game when it comes to helping users remove the Flashback malware from Mac OS X, but it has raised the bar for proactively protecting systems at the same time.