I agree with the order of events and likelihood but I just want to add something, and this is not a 'new' point. Kensil/Colts committed themselves to the stance that air pressure manipulation leads to a competitive advantage. Consider the events that took place under this assumption, and you start to see the malice of their actions. Certainly not ignorance of science as the OP suggested, my only point of contention with the post.
Assuming the OP's order of events, and assuming Kensil/Colts believe air pressure to be an advantage of somewhat significant importance.
Are we really to believe the Colts were willing to bargain their chances at a Super Bowl by letting this whole issue sit in the background while Kensil ran a sting operation? It's more important the Patriots be caught than the Colts advance to the Super Bowl? This is not believable. Something must be wrong with our assumption. No amount of contempt for a franchise would cause a team to forfeit a fair playing field in a game that leads to the Super Bowl. No one should disagree with that.
So we must assume then, the Colts do not believe this to be a competitive advantage.
So what about Kensil? Mike Kensil believes the air pressure to be vital to fair play, but is ready to allow a half, perhaps a whole championship game to take place while one team could very well be playing at a disadvantage. This also is not believable.
But then where does that leave us? Kensil and the Colts both do not believe any competitive advantage related to air pressure. Both parties are ignorant of science as we all agree, so they are convinced the Patriots are tampering with the footballs, and therefore must be convinced that the Patriots do indeed believe there to be a competitive advantage in manipulating air pressure.
We must change our assumption now, because clearly Colts/Kensil do not believe any competitive advantage to be gained in manipulating air pressure.
Given this information leading into the championship game, what is the correct action to take? Kensil should know the media will question the integrity of the game if he runs a sting operation allowing a lopsided game to play, even in part. Even though he and the Colts agree there is no competitive advantage, the media and non-Patriots fans will certainly jump on this. To me there is clear malice on part of Kensil and the Colts to attack another franchise over an issue they do not believe to be relevant. Kensil takes sole responsibility for gambling the integrity of the game(the perception of, not the actual integrity) in an anti-Patriot conspiracy. Kensil was fortunate the game was not won by a narrow margin, once it came to light science explained the deflated footballs, or the perception would have been much different.
Kensil's willingness to gamble on the integrity(perception of) of the game, even though he personally didn't believe it to be a competitive issue, or he did believe it to be a competitive issue but valued attacking the Patriots franchise over competitive fairness in a championship game are both terminating offenses in my book. I believe the Colt's can take the stance that they never believed this to be a competitive issue and left it in Kensil's hands, likely per his request, if they have any hard proof Kensil asked them to lay low they may get out of this unscathed, but shamed by the rest of the NFL organizations privately.