The Pats bring some interesting elements to the game of football. As I see it there are three possibilities:
(1) The Pats outright cheated and found a way for the ball attendant or someone else to deflate the balls after they were inspected.
(2) The Pats stretched the rules by inflating the balls with hot air so that they would initially comply but lose significant PSI in those weather conditions. (At least one meteorologist said that for every 10 degree temp drop, a ball could lose 1 psi.)
(3) The referee failed to do his job or in his judgment the balls were compliant. The rules state, "The Referee shall be the sole judge as to whether all balls offered for play comply with these specifications. A pump is to be furnished by the home club, and the balls shall remain under the supervision of the Referee until they are delivered to the ball attendant just prior to the start of the game."
Number (1) is the worst case obviously. If the Pats outright cheated, this will put not only BB under a cloud of suspicion, but Brady as well. Brady said in 2011 he likes deflated footballs, so one would assume he has a lot of say in how the balls are handled. In that case, the NFL would have to do something pretty drastic to restore the integrity of the game, and accept that the Superbowl would be tainted.
Number (2) and (3) aren't so bad. If the Pats complied with the letter of the rules but not the spirit of the rules, then the matter falls on the NFL for not having precise enough rules and on the refs for not doing a better check on the balls.
It's worth keeping in mind that the Vikings earlier in the year used heaters to warm their footballs (and were later simply told not to do it again) and Aaron Rodgers said he uses overinflated balls, so this has not been an issue that the NFL took with great seriousness until now.
My guess is that the NFL has no choice but to defend the Pats. The only way to protect the integrity of the game and ensure the profitability of the Superbowl is to say that the Pats followed the rules and the rules will need to be tightened for next season. Remember, the NFL is a business. It is not a system of justice. It will act in the interest of the game first, not right or wrong.
At any rate, I'll take a slightly tainted title over none at all. I think most fans would.