I'm happy to have stumbled on a nice project that allows creating ISO images from Java.
You can find it at http://jiic.berlios.de
Haven't had yet a chance of trying out the code to see if it can be used in lieu of the old mkisofs. However, reading the code at the test case already gives a good idea that it is suited for the task.
In the past, interacting with mkisofs has always been a troublesome relation. Just to keep things in context, I have been wrestling with the non-elegant mkisofs command line progress window for six years now: http://www.911cd.net/forums//index.php?showtopic=16829
Kudos to Jens Hatlak at http://jens.hatlak.de/