I just read some of the report (pages 75-90) and this actually does sound pretty suspicious. The excerpts that Deadspin chose to include in its article aren't really the most convincing parts, though.
After reading more, I do think they deflated the balls beneath the limit, and I do believe they did it at Brady's request. Having said that, I also think this whole case is still too flimsy to attach any meaningful punishment to it. I don't see anything in here that would qualify as 'proof' (and if there was, the headlines would be different right now). Just an apparent lie by Brady regarding his acquaintanceship with McNally, a series of suspicious-but-not-incriminating texts, and a lot of attempts to read between the lines.
So we'll see what happens next.