I've been thinking a bit more about this and in my opinion NZF have badly let their stakeholders down. In corporate terms, they've failed to maintain regulatory compliance. Even worse, they appear to have done so intentionally rather than through negligence. If what they've said is true then they knew they were potentially in the wrong in playing Wynne but they did it anyway (and if that's not true then why say it?).
The appropriate thing to do if there was any doubt whatsoever about eligibility would have been to approach FIFA and ask them. Then your possible outcomes are either that he can play, or he can't. The possible downside is you lose a leftback who isn't even signed to a pro club. On the other hand, if you just play him anyway you risk being pulled up, finding out that you were wrong and dealing with the ensuing mess.
We weren't challenged in a friendly, which isn't surprising because there's no reason to dig deeper, and any competitive match is too important to risk being awarded to the opposition because one of your team wasn't eligible. In my eyes, the damage from this is extreme in terms of NZF's reputation, and they've also robbed their players and fans of the Olympic dream. We're even more offside with OFC and FIFA than we were before too. And what about other players who might be eligible for NZ but haven't played yet - have NZF made themselves look like an organisation they would want to be associated with? Even if the amount of damage this does to NZF's reputation isn't as bad as I think, they need all the goodwill from potential players, the kiwi public, and the football world that they can get. As far as cost vs benefits go, not having Wynn would have seemed like a bargain compared to this clusterfudge. And it's not that hard to have seen that from the start.
To reiterate, the eligibility of players is NZF's responsibility. It's not FIFA's, it's not OFC's, it's not the players' themselves. If there was any doubt about any player's eligibility they should have approached FIFA. Even if they wriggle out of this on a technicality after a court case or two, that doesn't excuse a really stupid, unnecessary decision.