I only have a Librié and not a Sony Reader and if igorsk says it doesn't work with the reader, then I guess that this may not be an option. I have uploaded an example file with the popup window nevertheless and you can download it
here.
On the Librié you can press the "戻る" button to erase the pop up after you have scrolled over the superscript.
If you'll like to see the lrs source, it's
here. It won't compile directly as you'll need to change the CThumbnail tag to a valid thumbnail file.