Coach runs the show that's why it's on BB. There is no way there was a rogue equipment boy deflating balls. Can you prove who deflated the balls? Probably not, but it always goes back to the coach. The organization will definitely be punished but it happened on BB's watch. We're obviously not going to agree on this though I do agree Lynch would have to be the biggest moron on earth to wear the shoes but a suspension over shoes and no suspension over actual cheating just doesn't make sense to me.
Neither does suspending someone who you have no proof cheated. Hence a TEAM punishment. We know it happened, but we have no idea WHO. Hence, again, TEAM punishment.
Suspending Lynch would have made perfect sense had he not complied. They laid out a punishment right to his face, said if you do this you are out. Very clear. Makes perfect sense. Makes as much sense as any punishment ever. People go to jail over dumber stuff because they don't comply with very simple and easy things they need to do. As you said, ignorance isn't an excuse. They would not have suspended him for the shoes, they would have suspended him for not following a very simple "request".
Suspending BB for the Super Bowl, frankly, would be idiotic barring proof he did something, or gave the OK for it to happen. When a player uses roids do they suspend the coach? That is cheating right?
And regarding Lynch, had he pulled out the shoes and wore them for the game without anyone knowing about it before kickoff, he would have likely gotten fined, but zero chance of a suspension.