No. The Bottom Line is the NFL is a cash cow and Kraft has been on the receiving end of it. No matter what you think of Goodell as a commissioner, he has made the owners a #### ton of money. If Kraft takes this issue to court and wins, he damages Goodell, which likely leads to his resignation. There is no promise they find as shrewd of a businessman to negotiate their deals with the next commissioner, possibly costing the NFL money.
If Kraft takes this to court and loses, it would be a public admittance, backed up by a federal judges opinion, that the NFL champion cheated to win their trophy. This hurts the NFL image immensely and the Patriot's image even moreso. If the public doesn't think a sport is fair, they aren't likely to pay as much to watch it.(See baseball, post HGH scandals)
If you ever want to figure out the direction a businessman is going to go, follow the money. This was Kraft's Global Thermonuclear War. The only way to win was not to play and hope the public outcry goes away.