The Patriots did do something wrong, AND it was an NFL witch hunt.
When the story first broke back in January, Kraft had to fear the worst, if not fully expect it. Owners/members of other NFL owners are always sniping at the Patriots and Goodell, having a terrible year where he was perceived as weak and ineffective, was looking for any opportunity to look strong and in-charge.
Just a few days after the story broke, Kraft made the statement that ended with, "We will be totally exonerated and I expect a full apology." Belichick told of his crash course in ball inflation science and practice, and then reassured that there was nothing going on that broke the rules. Brady gave his tortured "What Me worry," presser and also assured that there was nothing done wrong.
Just a few days after that, the story of McNally being videotaped and going to the bathroom broke. At that point, we knew that a) The Patriots had done something wrong, and that b) There wasn't going to be any complete exoneration or full apology. It does not mean that Bob/Bill/Tom lied, but that, at least, their statements were not made with full knowledge of the situation. This understandable since they were preparing for the Super Bowl, but at that point, when they knew they had made inaccurate/incomplete statements to the press, they should have been in full damage control.
What that damage-control process was is not clear to me. They had to know, at that point, that there was a real risk that they could be rail-roaded. Was Kraft duped by Wells and Goodell? Possible, but I think Kraft is smart and very capable. Did they do their own internal investigation, discover something incriminating and decide to stonewall? That's speculation for Troll talk radio. But what did they do, after it became aware to them that McNally had taken the balls into the bathroom with him. Even if nothing was proven that he deflated the balls, that was still a violation that was going to incur some penalty. And that given the intent and opportunity, the NFL was going to have all sorts of opportunity to go on a witch hunt.
Sorry if all this has been stated before in one of the thousands of posts on the subject. But the issue to me is what strategy did the Patriots follow once they knew they were guilty of something and how effective was it?