You may be able to do what you want on your own machine given enough knowledge/time. The issue arises when a business based on a Mac Java app becomes redundant when Apple feels like it, or when it will become very hard to make a living selling an app Apple doesn't feel is right for the Store.
Once upon a time there was a company called Microsoft who controlled a popular OS. People who called themselves "hackers" generally didn't like it, since they asserted this power to control the product space as well, changing APIs or bundling software to eliminate competition. Apple has gone beyond Microsoft's wildest dreams, and are on track become comparably widespread - I don't think they get a pass just because the standby light has the same frequency as a human heartbeat.