Again, I really think that fans here are reading their narrative into a story that is likely significantly more complicated.
I just don't see Bob Kraft being like, yea take a 1st and 4th rounder (a massive disadvantage for the future of the franchise), a cool million, taint my name and my teams name, taint my hall of fame QB that gave us everything we have accomplished these last fifteen years and i'll simply roll over without exploring every possible solution.
Very likely he did explore every option, and came to the conclusion (for whatever reason) that it was not worth it to fight back in this setting.
I pretty much guarantee this is not about finances. At this level of power, he stands to lose much more from fan reaction than anything Goodell can promise him. Further at the end of the day, knowing some very rich people myself, their general concern is almost never about more money and almost always about legacy and what their product actually does for the world.
My theory is that his lawyers told him that suing the NFL would just drag the Patriots name in the mud for a few years with very little chance of winning. Worse, getting the case dismissed by a pro NFL judge could look bad for our case (which is really a case for public opinion, something we are currently losing).
Perhaps he thought that the resolution of the Brady appeal, which is much more favorable to us, would do the job for him and that pursuing his own appeal would make that case worse.