I agree, a ruling like that would be batsh*t crazy absurd. But it may be the best resolution available.
If Goodell totally exonerates the Pats and there is no penalty at all. Several teams and most of the national press, even the mainstream press, will go totally bonkers. Remember the feeding frenzy before the Super Bowl. Goodell would never shake the implication that he's Kraft's toady. And the Pats would never escape the allegation of wrongdoing, but they have "Goodell in their pocket". Lose-lose.
If Goodell comes down hard on the Pats without ironclad evidence of wrongdoing. Kraft goes ballistic, Goodell loses his support, the league loses his help and support, and the ruling gets overturned on appeal for lack of evidence. But our reputation gets tainted forever for no good reason. Lose-lose.
Or maybe Goodell gives both sides half a loaf. A small fine for an equipment violation. While making clear the cause for the underpressure footballs was environmental. Then tightens up procedures around ball pressure and security (different protocol for inflation and ball security pre-game, routine halftime checks, adjustments by the refs as necessary). Goodell then announces that Mike Kensil has been reassigned to the new "Center for Equipment Compliance and Environmental Research" to be created especially for him in Novossibirsk, Siberia.
Those out for Patriots blood no longer have a leg to stand on. And the Pats appeal the fine and easily win. Partial win all around.
To paraphrase Bill Cosby: Comissioners, like parents, aren't interested in justice. They just want peace and quiet!