I use Atmel's AVRISP MkII, it will everything you ask and works well with AVRDude so all you would have to do is write a short batch file and the users could very easily do what you need. If you need a GUI to do the tasks you could download AVR Studio, Atmel's free IDE.
Here is a link to the MkII http://www.mouser.com/ProductDetail/Atmel/ATAVRISP2/?qs=sGAEpiMZZMuk%252b7HJuOzfqFcX98cO1Rkac1lDVM1BSh4%3D
wade