As best as I can tell, the key facts mentioned in the article are:
i. A woman accused a Freo official of inappropriate behaviour.
ii. The club and the woman agreed a financial settlement.
iii. The AFL completed an investigation and imposed no sanction.
iv. The woman doesn't want to talk about it (or possibly can't).
You could read anything or nothing into those facts: it could be a misunderstanding blown out of proportion by a tabloid, or lecherous behaviour by a creep that was covered up by the club. How would you know?
Shane's point is pertinent: one of the difficulties with these situations is that we put the complainant in the position of having to decide whether to accept a confidential settlement so they can move on with their lives, or make a public complaint with the much lower prospect of compensation and a very high prospect of further repercussions. You can't blame people for agreeing a settlement, but it generally means the accused goes (relatively) unpunished.
Sadly, leaving it to News Corp to handle the inherent sensitivities of these situations doesn't help anyone.