Correct me if I am wrong but Amiga's DB9 joystick port does not support mouse wheel - there is just not enough pins for it? To get wheel support one must use either serial mouse (+driver) or some custom adapter (+driver) which feeds wheel related events to the Amiga via joystick port. After you somehow manage to input wheel events to the Amiga only then you can use software like FreeWheel, no?
Now what would be really, really really cool would be a Rys MKII like adapter, which connects to both DB9 ports and would have three USB-ports; two for joysticks and one for the mouse. Adapter would have three modes, joystick + joystick, mouse + joystick and wheel mouse. Modes could be switched just by pressing mouse button or joystick's fire button.
There should be no technical reason why this could not be done and even drivers for reading wheel events via joystick port exists in the Aminet. Anyone wanting to take the challenge? Rys MKIII perhaps?