If I understand correctly, the 11 balls were deflated by 2 PSI from the pre-game check to the in-game check.
That seems fairly significant, and it's pretty clear circumstantial proof of tampering. If the Colts balls were fine, this seems like a pretty obvious attempt to gain an advantage by cheating.
Is this a morally huge deal? I don't think so; I see it as similar to baseball teams that wet their infields, or let the grass grow long.
However, when you knowingly mislead the officials by tampering with the balls after the initial check, I think that becomes a big deal.
This isn't going to hurt the Pats in the least going into the Super Bowl, though. They're ultra-focused, and they thrive on the "us against the world" stuff.