IMHO it is one of the big tragedies of modern IT history, that JavaScript and Python 'own' the market for scripting languages in the mainstream.
From a pure technical perspective, I would guess JRuby or one of the JavaScript implementations would have been a better choice for scripting, especially given the poor state of Jython.
From a pragmatic perspective and what your users are mostly able to figure out, Python might have been the best choice. I even saw software developers with years of experience in imperative languages struggling to understand Rubys blocks...
Out of pure interest: What was the purpose of the Java application and which aspects did you allow the users of the application to script with Jython?