It is two different issues.
1. did them deflating the ball cause the Patriots and unfair advantage which caused them to win the game. Absolutely not. Blunt could have been carrying a cement block and still gone through that defense.
2. Was it breaking a rule, and were they caught breaking said rule. From the evidence so far, it appears so. Regardless if it help them when the game or not it is a violation of the rule book. Each team is given 12 "game balls", the Patriots had 11 of their 12 found to be deflated. We do not have evidence at least publicly on the Indianapolis side.
The Colts lost that game regardless of the deflated balls. To "protect the shield" the NFL will need to punish the Patriots at this point, and hopefully they do a better job investigating and explaining than they did about the Ray Rice issue.