I find the easiest way to exit... and keep the terminal window open is to Ctrl+Backspace.. then go back into the mupen64 window.. and before it flicks back to fullscreen hit the power key... then End Current Task will show up in the drop down menu.

On another note... I've been screwing around with Accelemymote today, trying to get accelerometer working with the emulator, but I can't... and I've no way of even knowing if accelemymote is even working as I don't know what to test it with. For anyone trying... you need to reboot after installing it or else you will get segmentation faults trying to start the emulator.