Some perfectly legal deflation of the balls is apparently part of the process of preparing the balls based on the fact that in one Jets game, it was discovered that the balls that were given to Brady to play with were at 16 Psig. We don't know exactly what the temperature was when the balls measured 16 psig but this is far enough above the maximum range of 13.5 psig that unless the balls were 150F or something like that, the balls were either delivered over-pressurized or over pumped somewhere along the way.
Deflating balls before the refs check the balls is fine, it is only deflating balls after the refs check the balls that would be a violation of the integrity of the game (sarcasm). In the particular case for which Brady was suspended, there is no evidence that the balls were deflated after inspection by the refs. In fact the half time measurements (ignoring all other evidence) make it more probable than not that the balls were not deflated in any way.
All of the other evidence is just noise. If they had found that the Patriots balls were consistently and unambiguously deflated by say 2 psig (hmmm, where have I heard that), then I would look at all of the other evidence (text quotes and visit to bathroom) differently. But there is no body here and in fact the person suspected of being murdered turned up in good health. Yet someone is on trial because a colleague of the suspect sent a text to another colleague where he claimed in a very general sense, to be a "killer" and there are 90 seconds where he can't account for his whereabouts. Ergo, they must have done something; there must be a conspiracy.
The Mortensen leak in particular framed public opinion and from then on, people have been a victim of confirmation bias. It is very hard to change your mind on something like this. It is just how people are wired. Had the first reports been, "the balls have been measured and appear to be in the expect range when temperature is taken into consideration but we have some suspicious texts and a suspicious visit to the bathroom so we are investigating", wouldn't that have dramatically changed the narrative from that point forward?
I am an engineer and I work with the ideal gas law (and other gas laws) so I understand gas laws much better than I understand jurisprudence law. When I heard the story that the balls were tested and (whatever it was) 13 of 16 were 2 psig under, my first thought was how were the balls tested but I am sure that I am in the vast minority on that. It did not sound good for the Pats based on those early reports, that is for sure and if you formed an opinion based on that information (which I think it is fair to say that the vast majority did), it is going to be much harder for you to change your opinion.
This is especially true for the NFL Execs. They not only formed their opinions but in some cases went public, in other cases made private statements (we gotcha) and in all cases put in motion an expensive and elaborate investigation and penalty process that was supposed to provide confirmation that all these execs were right all along. It is no longer about anything else other than proving the NFL execs were right all along.