I'm pretty sure that a table calculation that calculated the proper median could be created. That would then be placed on the Level of Detail shelf and then you could add the reference line.
If you're new to table calculations, you can start here http://kb.tableausoftware.com/articles/knowledgebase/table-calculations. If you need help, I'd suggest post a packaged workbook with some sample data.
Thanks Jonathan, it took some trial and error with "Compute using..." in the table calc, but I was able to get it to work. Much appreciated!