deflating the balls, a much larger number of people would still have to be aware that the balls were deflated and didn't say or do anything about it for years. Many of those people have no allegiance to the Pats, so pissing off Belicheck or Brady wouldn't mean anything to them, in fact it might be an added bonus.
My suspicion (which I have no evidence for) is that the Pats have probably been doing this for years, and that the refs "pregame check" of the balls consists of a ref squeezing some of the balls and declaring them fit for play rather than putting an actual gauge on them to confirm that they're legal. Maybe a few of the teams over or under inflate the balls, and if the standard isn't strictly enforced, the balls tend to be inconsistent from team to team which is why no one, including the refs, actually said anything until they were called on it. I think it's more than possible that the balls were simply submitted under-inflated and the refs half-assed the pregame check. It doesn't clear the Pats at all, but it seems like it would be a rather simple explanation about what happened to the balls in the Colts game... Of course, the Pats will never admit to submitting under inflated balls and the refs won't admit to half-assing the pregame check, so instead we have a bunch of sports reporters and college professors trying to apply the Ideal Gas Law, which explains how changes in temperature affect pressure, to make their arguments.