It's not as specific as that (at least not from my perspective). Any professional league in Australia will revoke a journalists access if they bring to light things that significantly undermine the league's power brokers. The journalists have to weigh up the benefit of publishing something scathing and/or undermining with the risk that they will lose access to players, coaches, clubs, that offers them material to generate easy content.
It's much easier to produce "good enough" content from inside the purple circle, than it is to do so outside it. Being freelance gives you more flexibility in this regard, but not complete freedom, because the same applies. But if you work for a media agency, and you burn your ability to generate simple/basic content, you're employer won't be happy with you.
It's not cloak and dagger where Rugari gets a yellow envelope in a car park at night from some shadowy figure from the APL. It's simply known not to bite the hand that feeds you. It's an alignment of common interest - I want to maintain my access to players and clubs, and the league wants their power to not be undercut by the media.
Access comes at a price, and if you don't think that influences what journalists publish, I applaud your sincerity and integrity. Having said all that, I can't speak to what motivates Rugari. He may genuinely think the A1/A2 split option is the best, but we have reason to be skeptical. Further, Windley is promoting a model he thinks is the most likely to work, not necessarily one he likes the most. He has said almost exactly that. He's being pragmatic and I can appreciate the motivation for doing so - but I don't think it will be sustainable and therefore will do more damage in the long run.