I understand what it's like to be accused of something you never did, resulting in a dumbstruck response to said accusations.
In these situations, I have both confronted and fought (mostly figuratively, once literally) the person and have also tried my best to ignore the accusations. When dealing with someone with more power than you, both responses are almost always a losing battle (even if you win a fight, you can most certainly still end up doing more damage to your reputation and well-being e.g. Al Davis and drunk frat boys).
I think the biggest (or only) sin that Bob committed was not being proactive - "Fool me once...." After Spygate, he should have known the patriots were treated unfairly, and should have been ready for more unreasonable accusations from the NFL. Sure, the pats taped from the wrong spot. They did commit a foul, as minor as it was, so they had to own up to it. But the punishment should have raised every single eyebrow in the organization.... we were punished worse than the Broncos after their cheating in '96-'98 apparently coincided with 2 super bowl wins.
I think the only way Kraft, Belichick and the rest of the organization were proactive was by being more conscious of the rules - worrying about their side of things, not how to prevent the unreasonable actions of the NFL. I don't know how anyone could have been prepared for the ******** that the NFL invented.
Yes, Kraft had absolutely no backbone, and was too trigger shy to stand up for people he trusts. So, how do you confidently defend the actions of a whole organization of people without knowing absolutely no one did anything wrong...... I'll tell you how, you pay millions of dollars to investigate and find out exactly what happened. Luckily, the NFL did that for him, and he hasn't run with all the information he was given.
Without defending or condemning RK, I feel like Goodell committed murder, Kraft was left holding the gun, and then he shot himself in the foot to boot (no pun intended). He knew he was fighting a losing battle, and he fought it the wrong way.
Bob's the owner and ultimately the blame should fall on him, but it pisses me off that Goodell was able to make us Patriots fans ashamed of our own organization for completely made up circumstances.