I still hesitate to condemn Kraft, especially since we lack full knowledge of the dynamics and politics of what goes on inside the NFL. We can only speculate. What little is known is sufficient to recognize that there is an acrimonious feeling of resentment against the Patriots, and in particular Belichick and Brady. As others here have indicated, Kraft is a businessman, and knows when to roll with the punches and when to jab. I suspect that he would rather lose Deflategate, than win and build up even more resentment. The consequences could be even worse than the team has already experienced, including amplifications of media bias, referee miscalls, inspections, drug tests, unfavorable scheduling, communication monitoring (legal and otherwise), draconian punishments and of course additional sting operations. As public sentiment slowly changes to accept that the punishments were harsh, then as long as they stand the internal resentment will gradually dissipate, and the nightmare scenario above will evaporate. Or at least that is what Kraft may be thinking. But this too is speculation, and I admit that I am too ignorant of the entirety of the situation to make a binary judgement.
Where I do feel that Kraft could have done more is with the Brady case. The Wellsreportincontext site is great for fans and supporters already convinced of team and individual innocence, but it does little to sway overall public opinion. It is a passive approach, where a proactive one is sorely needed. In particular Kraft should be publicly demanding that the NFL separates the issue of CBA authority, as featured in their appeal, from the the Deflategate case in general. Too many see the current court case as as a question of Brady's guilt or innocence, and that is the biggest travesty of all this misspent currency. Becker's Amicus Curia brief should be the vehicle for Kraft's unequivocal support and action to protect his greatest asset, TB12 and his legacy. Accept the fines and the lost draft picks, but agree there is no basis for the court case, IGL is a natural law and cannot be compromised. Some blood has been spilled, which should satisfy the jackals in the NFL, but the Patriots are strong enough to overcome the penalties.
Just win a few more Lombardis despite the injustice.