Cows fans won't like this opinion probably but that run to the finals/GF last year has really done a number on them, both mentally (as Mackey says above) and physically. They gut checked the shit out of that run of wins, and while they did get lucky with Merge tripping over their own feet, they still showed in every game that they would be pushing themselves to the limit under great duress to stay competitive. In retrospect, this proved to be a poor decision.
Sure you can't expect them to just keel over and die in front of their fans in a finals series, but a tad bit of foresight from Green wouldn't have gone astray either. Making your players physically belt themselves to make a GF they can't possibly win was always going to have repercussions. The nosedive decline of Thurston has just made things worse.