I don't think it's an AFL conspiracy. Gray's a big name player and therefore the incident attracted a lot of commentary. It seems to me that the club played this well - there really wasn't any argument about the tackle, it was an unnecessary sideways sling. The MRO geezer had publicly called it a dangerous action and sent it straight to the tribunal because guidelines only allowed him to impose a maximum 2 week penalty and the tribunal's penalties start at 3 weeks.
Best course of action was to do as Shane notes: be contrite. Turn up, say " you got me, I'm guilty" and plead your case for a minimum penalty. In fairness to the club, they did use footage to demonstrate that Gray's arms weren't pinned, and that he could have braced himself for the impact, but didn't.
Maybe the team were sent out on Sunday with an instruction to make Port know they'd been tackled hard, and make them earn each and every ball and Nyhuis just went a bit too hard, this one time.