I suggest the following solution, I'd like to get Harvey's opinion:
- Java3D 1.6 pre 13 remains frozen with a few bugs and this limitation under OS X
- Java3D 1.7 uses another namespace instead of "javax.media" and includes some goodies (more type safe methods, relies on Java 1.7, drops support of Java 1.6)
Then, the developers who would like to support OS X 10.11 would be forced to switch to Java3D 1.7.
However, ctrueden, note that the extension mechanism has been dropped in Java 1.9, you'll have to make some other changes to go on using AppleScript. That's why another solution consists in changing nothing within Java3D. You can bundle your own JRE with your software.
I'll have to update my tutorial very soon.