Not being an Australian, I don't entirely understand this AFR vs league thing you have going on, and am not knowledgeable on the AFL's problems.
But, to take the article as league bashing by an AFL person is naive - the problems are real, and unpleasant - irrespective of what goes on in any other sports (clearly, many sports have problems). If you think there is not a problem with the players, and the culture more generally, or think that the response to any criticism is to say "well it's just as bad in AFL", then, respectfully, you are part of the problem rather than the solution.
The culture has to change - end of story - AFL problems are for AFL to sort out, and the same with union etc. Warren Ryan gave a great interview on radio in NZ the other day - the full-time professional era has created new problems, and they haven't been addressed. Sorry, but Knightmare's letter might incite some feelings of vindication for you and your "attacked sport", but it reads as defensive and a bit sad really.
If Smith's article was an AFL person taking cheap shots at league - then I understand the frustration. BUT - there are huge problems in league, the attitudes of the players and many club officials (Gould even said his first response was to believe and support his players). In many cases, these guys have dispicable attitudes towards women in particular, and anyone outside of their "illustrious" group. I love watching league, and repect their atheletic ability - but, in reality they are not people to be looked up to, they have been irresponsible, immature, believe that different social/moral/professional standards apply to them, and are clearly very stupid in many cases. Fortunately, many players don't fall into that category, but all are tarred by the lowest common denominator.