The existence of the report was not confidential, just its details. It's perfectly normal, and I consider in this case advisable, for an organisation's report to remain confidential, especially when you are hoping for individuals to be candid about illegal activities.
One of the outcomes of this report was that the Eagles remained on probation, and were effectively given a suspended sentence, such that any further recurrence would lead to action by the AFL. Cousins was in fact banned for a year in 2008 for bringing the game into disrepute. The details of this report would have played a role in that decision by the AFL.
It's not the AFL's job to be the media or the police. In 2007 the police had enough trouble pinning crimes and misdemeanours to the Eagles players. Do you expect the AFL to do better than the police force?
The report suggests that the Eagles didn't do enough given the rumours flying around, and Gillard found it hard to believe the Eagles didn't know more than they let on. That's a reasonable opinion if you ask me, but it is still just an opinion, and it is one based a great deal on hearsay.
Now, if you think people should lose their highly paid careers based on rumours and opinions, well fair play to you. But I wouldn't be advising a sporting administrative body to take such action.
The Eagles were wilfully ignorant and gutless, and Nissy and Woosy will have to live with their decisions. But suggestions that the AFL should have publicly intervened and investigated in parallel to the police are misplaced.