I'm guessing Apple's plan involves Gatekeeper (coming soon) and not shipping OS X with Java and Flash by default (already implemented, but installing both is ridicoulously easy). I'm not sure how teneable and wise that is, though.
That won't help the people who actually use Java on OS X. It would be better to allow Oracle to manage the updates for Java on OS X, the vulnerability that Flashback abused was patched by Oracle back in February.