Goodell's in a tight spot. Fans of 31 teams are screaming for a major punishment so a somewhat minor penalty, say a second and fifth round pick forfeiture, is going to have those fans calling preferential treatment.
The other popular penalty floating around online is the suspension of Little Bill. That along with a few picks would probably placate most fans but it's already Wednesday afternoon. If he ultimately decides on a suspension, he'd almost have to make that decision quickly. If Belicheat gets suspended but it doesn't take effect until after the Chargers game, people again will cry about the perceived preferential treatment the Patriots are getting.
That San Diego game is coming down as one of the most important in Patriots history. They need to win and they need to play very well in the second half or everyone's really going to question their recent past. There's not going to be enough polish on the planet to remove the tarnish. Of course no one but Dallas fans seem to care that San Fransisco bought themselves a Super Bowl by circumventing the cap but that was before the huge surge in message boards and sites like PFT always looking for a story to beat to death.
I think the best analogy I've seen regarding this fiasco involves poker. This is like the Patriots sitting at the final table and being the only one able to see the other player's hole cards. They wouldn't win every hand thanks to how the flop fell but they'd have a distinct advantage over the long haul.
I think the most damning bit of evidence about how this may have helped the Patriots is last year's AFC championship game. Patriots were up big then, contrary to their history of quality second half adjustments, they fell apart. I doubt it was a coincidence that it was the first time someone ever banned all cameramen from the field like the Colts did.