This becomes a contractual/legal matter and the NFL, for as powerful as they are, cannot invalidate the Patriots rights.
Do you really think Goodell would offer up an agreement for Walsh that Kraft hadn't seen and agreed to? Goodell is a representative of the owners, not the head of an entity policing them (as many seem to believe).
I doubt Walsh has anything substantive to offer. If he did have something damaging (Rams walkthrough or similar) and could pin it to Belichick, I think Belichick would immediately be fired by Kraft and suspended by the league (in case someone hired him). Again, this would be Goodell and Kraft working together to come to a resolution to the issue that would allow the Patriots and the league to move forward.
Look back at this whole affair and you will likely see a cooperative effort by Kraft and Goodell, balancing the integrity of the league and the effects on the Pats:
1) Loss of 1st round pick as punishment? After some convincing, Kraft probably agreed that a lesser punishment would be seen as weak, given the 2 1st round picks and probable late drafting position. Doesn't make it fair, but it is what it is.
2) Examination and destruction of evidence in Foxboro? I doubt Kraft would let any of his property out of his control after seeing his seized property broadcast on Fox. The reason why Goodell's explanation of the handling of evidence seems contrived is because it is. Kraft dictated the terms and Goodell followed them. Goodell could never admit that without getting destroyed by the media and Congress.
3) Not interviewing Walsh? Again, Kraft didn't want the NFL investigators anywhere near a rogue former employee with an ax to grind.
Probably more examples but you get the point. Kraft has been protecting his interests all along and doing it in a way to keep the league united...and letting his buddy Roger keep the bad cop image that is actually a benefit when dealing with folks like Specter. Kraft deserves a pat on the back. He certainly doesn't deserve accusations that he is bending over and taking it willing from Goodell (not saying you were doing this, EBU).