1) Because the leaked information only goes back to 2007 -- the year during which Frank Coonelly took over as team president -- we have minimal insight into the organization's finances, how they ran and what they looked like prior to Coonelly taking over. This means we know almost nothing about the way the team was managed during the McClatchy years, apart from how much gents like Derek Bell and Jeromy Burnitz took home. Because we don't have this information, we don't have much context with which to judge the efficacy of the Coonelly operation.
2) After reviewing the AP story, the PG's coverage, a local CPA's analysis of the books, and the financial documents themselves, it seems to me like the Pirates under Coonelly and Neal Huntington are doing exactly what they say they've been doing all along. See Franco's post below for a general outline of what we feel that strategy has been.
3) While organizations will occasionally leak their own information as a matter of PR strategy, this leak doesn't appear to have come from the Pirates. In fact, it looks like it was designed to smear the Pirates. The quick and easy message here was that the Pirates have been profitable while fielding a crappy baseball team. When you toss in that the leak was to the AP and not a preferred local media outlet, such as the Post-Gazette, and that the AP also obtained a check stub from a payment made by the Pirates to Seven Springs, the Nutting family-owned ski resort, that's only going to fuel the long-running, local speculation that the Nuttings have been filtering money from the ball club to other ventures for some time. There was just enough information leaked to make the club look bad at first glance whether they're doing things right now or not, and most of the people who will read about this won't give it more than one glance. My money is on Major League Baseball as the source of this leak, as the league would have had all these documents from the independent audits they do of each team's finances, and that it was designed as a warning shot to get the Pirates to make some kind of significant payroll increase at the major league level.