Further to this request I have made a little hack which allows glossary definitions to be displayed as tooltips rather than as a hyperlink to a pop-up window. You can see the results in the attached screenshot, showing 2 options for the tooltip display.
If you are interested you can go see the full description in the tracker MDL-18213, you can vote for it or download the attached files and try it out on your own moodle test server.
Hope this will be useful,
Joseph