Thanks Jon, MagicPrefs has at least provided a workaround. Among the options is an ability to disable or enable one finger, two finger, or three finger scrolling. Disabling one finger scrolling and enabling two finger helps prevent the jumpiness I was experiencing from inadvertent movements of my finger on the top of the Magic Mouse. I'm not sure I am completely happy with having to use two fingers for all scrolling, but at least it is a workaround. Gaining the ability to zoom in and out with a finger pinch or spread as on the iPhone is a nice bonus. There is also a touch sensitivity adjustment and I am going to see if that will let me go back to one finger scrolling without Java hypersensitivity.
I would still like to know why that hypersensitivity only appears in Java applications.