I believe they would have defeated the Colts easily without cheating. But they cheated. Trying to cheat your way into the big game should not be permitted.
For example, in baseball when a player gets caught using a "juiced" bat, the player is penalized.
So it follows, in football when a quarterback gets caught using a "juiced" football, the quarterback should be penalized.
After all, "juiced" equipment is "juiced" because an individual player wants it that way.
He's not likely gonna tell the coach about it.
I can only say that in sports where the money isn't huge, the penalties for cheating are (huge, that is). Cheaters are often DQ'd and some are banned from the sport for a period of time or even for life. That being said, in the NFL, the penalties are so comparatively mild that it doesn't discourage the practice.