So CPython is EOL, but that is a different project then Java Python. There is also a Go Python... We are discussing introducing Groovy as an alternative, but it's not clear right now what version that will go into.
There is no problem with Jython. It is mostly connective code. You can keep most of your business logic in Java and import those classes into the Jython scripts. I would advise to keep the Jython scripts short.