The one big problem with this one:
As we've seen time and time again, emotion is a big part of the game of football. A team beaten up in the first half can be in real danger of giving up and rolling over in the 2nd half.
So the first half taints the second half even with properly inflated balls in the latter. So it really isn't all that improbable that Indy could have won in a fair game. We'll never know because we can't imply anything from the unfair game to the fair game.
Plus, as stated by me and others, cheaters deserve to lose even if they won 200-0 anyway.