This is when it's nice to have the league's most influential owner.
Goodell is still in new to the commissioner's job. If he is seen as favoring the Krafts, it will undermine him down the road, when he has to negotiate a new revenue sharing formula as part of the next CBA negotiations.
I think he is MORE likely to give the Patriots a serious punishment than another team which did the same things.
IF the Patriots have been caught red handed, I would expect them to lose a sixth or a seventh, plus a fine for the club and a suspension for some demonstratively involved individual.
For any other club, I would have expected a seventh at the very worst, and more likely just a fine and suspension.
If Goodell doesn't hold the Patriots to a higher standard, he will regret it.
Moreover, if Kraft actually owned Goodell (which he doesn't) he would be smart enough to tell Goodell not to give him any favors. Kraft will need to call in his markers when the next revenue sharing agreement is negotiated, and anything he does to strengthen Goodell now will increase the value of those markers then.