Currently the way javatoolkit is packaged and installed is lacking. Plan is to move javatoolkit into pythons site_packages and install the binary packages into /usr/$(get_libdir)/javatoolkit/bin. Support for this within eclasses will be coming shortly. Once this occurs I will merge the svn branch that has a better project structure and bump the package.
Should have actually updated this ages ago. Support within eclasses and ~arch javatoolkit package available. This bug will be closed when latest javatoolkit stablised.
0.3.0-r2 is now stable