Following its release of Java for Mac OS X 10.6 Release 3 (10.5 R8), Apple stated that “the version of Java that is ported by Apple, and that ships with Mac OS X, is deprecated”. Apple has long been producing its own Java runtime, and Java was originally brought to Mac OS X with the aim attracting Java developers to the platform. Since Java application failed to take off, and Apple’s own Cocoa has proven to be extremely successful, they have no real incentive to maintain Java themselves.
This doesn’t mean that Java will disappear from OSX, but instead will allow third parties, such as Oracle (who recently purchased Sun) to provide their own Java runtime directly. The Java Preferences app will allow users to manage the different versions of Java that are installed.
From a security perspective, there is one distinct benefit of this change: faster updates. Apple has always been slower to release security updates, and this will allow those updates to reach Mac OS X users in a much more timely basis.