Over the past two months, there have been a few good articles written on the concept of using Jython within Java apps without utilizing the jythonc utility. This is, in fact, the best way to invoke Jython code within a Java app.
Read more about using this technique in these articles written for the Jython Monthly newsletter.
Accessing Jython from Java Without Using Jythonc
Simple and Efficient Jython Object Factories