Good to know it works, but it must be a pain to shut it down like that. I find it a bit strange that a Java app can bring down the OS like that, it's supposed to be completely separated.
But I have noticed some instances where the JavaMO seems to hang when closing it on my SE also. I think it is because it is busy receiving(or waiting, if bad connection) for data. I will put it on my list and check it out. Maybe it will help on your problem too.
On my phone, I can press the "switch app" button, and select "End app" (or similar) to forcefully close the MO. Maybe there is some similar function on the BB?
One other thing: How are the key mappings? If you find that you prefer a different key mapping, you could download hari's keycode jar (see some other post in this thread), and list the keycodes for each key, and what you would like it to do.