The simple answer would be to say that the player is actually an employee of the AFL and not the club itself, therefore he will play within a side chosen by the rules dictated by them. In a sense, players would be leased from the AFL, rather than being "owned" by the clubs. I don't see why this couldn't be the case, as it currently is "assets" such as club logos and merchandising rights are already owned by the AFL. This wouldn't really be any different.
The most frustrating thing about the whole Judd saga was that it looked like he was going to choose Collingwood, and the rich would get richer. In the end he chose Carlton because they were able to provide him the most attractive salary package. Why? Because it would seem Dick Pratt's paying him and his lovely girlfriend in ways other than through the footy club, thus circumventing the salary cap. The salary cap is chock-a-block full of loopholes that the rich clubs can exploit, and the poor clubs, like us, can't.
In FA, we would just see more and more of this. All the best players flock to one club and all the poor clubs rot. You see it happen in grassroots footy as well.