This may not apply to you just yet, but I recently have been working on Clamp, a package that supports this requirement. Clamp - and its name! - builds on earlier work by Darjus Loktevic and Charlie Groves.
Clamp can be found here, https://github.com/jythontools/clamp
, with Clamp's usage documented in this demo project: https://github.com/jimbaker/clamped
. Although currently you need to use GitHub to access, Clamp will be in PyPI once we have beta 2 of Jython 2.7 out. Jython 2.7b2 in turn requires supporting both pip and and its remaining (somewhat challenging) dependency, nonblocking SSL sockets.
In particular for your use case, Clamp adds a singlejar command to setup.py such that if your code has a __run__.py file, the jar is a single executable. Alternatively, such "uber jars" can be used by frameworks like Storm or Cassandra (specifically triggers). Clamp also covers a bunch of other use cases for Java integration, including being a compelling replacement for the Jython object factory pattern.