All the latest update does is disable the plug-in and remove Java Preferences.app from your Utilities folder.
It does do that but it also "delivers improved security, reliability, and compatibility by updating Java SE 6 to 1.6.0_37." -Java for OS X 2012-006.
Also, make sure to study design patterns... these are general design strategies and algorithms that are not specific to language, and they are far more important to understand than the simple mechanics of whatever language you're using.
Thomas is right. The only thing I can add is that there are established "camps" in the industry. Java is one of those camps. Microsoft is another one. In theory, what you learn from one language will help your understand of other languages. It's all just syntax. In practice, you have to be careful to avoid getting pidgeonholed as a "Java programmer" or a "Microsoft programmer". If that happens, you don't get out. Even though it is a smaller market, sticking with UNIX and C will give you more options. You could still do Java or Microsoft if you had to, but you wouldn't be shut out from more interesting work.
There isn't too much institutionalized Objective-C, Mac, or iOS training available. In spite of Apple's popularity and market presence, Apple has zero respect in the enterprise, and that includes the education enterprise. Linux and especially Android get support, but if you want to learn Apple technologies, you will be pretty much on your own. There is a Developer forum here on Apple Support Communities and more extensive developer forums in the paid Developer programs.
Learn the basics, focus on UNIX and C. Do all your own on your Mac and learn Apple technologies on your own, leveraging what you are learning in school.