No, you don't have to dispose of objects. However, you must take care that stale versions of your jython objects don't get stuck in memory by references elsewhere. See this comment for some general advice:
In my experience, Ignition settles to lower RAM usage with G1GC than with the CMS default. But wherever it settles (peak of the sawtooth in a usage trend) should be encompassed by your initmemory. I'm not sure there's ever value in having init memory != max memory -- just let Ignition grab the memory you want it have up front and keep it out of the grubby hands of competing processes.