I'm not agreeing with Kraft's decision. I was incredibly disappointed by it. And in the end, he was wrong. But it's pretty easy to understand how he thought it might help. Again, not agreeing with it, but it wasn't a crazy thought. It was pretty rational actually.
In essence, Kraft was giving Goodell a way to save face without having to go after Brady. Goodell and the NFL blew up this issue to ridiculous proportions. At the time, we had no idea what was true or not due to all the leaks and the league intentionally withholding key information. Then it turned out to be a ridiculous farce. By that point, Goodell's ego wouldn't let him just shrug it off. He needed blood to justify everything or admit he was wrong.
By conceding a pound of flesh from the Patriots, Kraft was allowing Goodell to tell the owners he had done his job, even though he botched it. If he had stopped there, the owners would have been satisfied, the team would have been heavily-penalized, the rest of the world would have assumed us guilty of all charges in this kangaroo court, and Brady would have been spared. It actually makes a lot of sense.
Where it went awry was Goodell getting greedy and using this to try and leverage the league vs. the NFLPA. It became more about the CBA and future battles after he got his ass handed to him in the Peterson and Rice cases, and he wanted to prove his authority to the NFLPA.
Obviously it was a terrible decision by Kraft. I absolutely hated it when he made it, and it still disgusts me today. But his thought process is understandable, even if I disagree with it.
