It is probably easiest to bundle MMJ in the app, since it seems that JNI libraries can not be loaded directly as a JAR resource.
Because MMJ is licensed under CC BY-NC-ND terms, this can not be done by the default build; a build flag should be added along with a note that by including MMJ the CC BY-NC-ND terms apply. When the build flag is enabled, dynamically update the LICENSE file of that build accordingly.
Alternatively, it may be easier to just move OS X packaging into a separate project, and license that project under CC BY-NC-ND as well... However then the whole OS X build would fall under that license :/, so maybe not.
Also the fact that the CC BY-NC-ND terms apply for the OS X distribution needs to be mentioned on the website.
Some Mac OS X packages include Humatic’s MMJ, developed by N. Peters. This driver fixes an issue with the Java MIDI system on Mac OS X. This library is licensed under the Creative Commons BY-NC-ND license. Please be advised that this library can not be distributed commercially, and as such these OS X builds do not fall under the Apache License 2.0 license terms. Visit http://www.humatic.de/htools/mmj.htm for more information.