You are quite correct that Kraft was wrong to support Goodell for all those years. Even Kraft has admitted as much.
That being said, it was totally on Goodell as to why draft picks were taken from the Patriots for totally unproven allegations of minor cheating.
Goodell has now clearly been exposed for who he is - if anyone is really listening. And yet we have owners like the Houston Texans owner that continue to misunderstand (at best) or deny what is so obvious to those of us who have studied the facts. It will take quite a bit to get rid of Goodell, probably a lot more than what has already happened. The owners are that ignorant. It's not implausible at all to think the exact same thing would have happened even if Kraft had wised up 8 years earlier in 2007.