No doubt payroll is an issue, but also no doubt that SI doesn't know what it's talking about. Littlefield didn't "acquire" Mike Gonzalez, except in that he stupidly lost Gonzalez in a trade and was able to get him back a few days later when it turned out that Brandon Lyon's arm was balky. And no matter that, as a poster at Primer pointed out, Littlefield's Pirates have lost Brian Giles, Aramis Ramirez, Jason Schmidt, Chris Young, Bronson Arroyo, Craig Wilson, Kris Benson, Dave Williams, Damaso Marte and many others, and only managed to get one good player who's still in the organization in return for all those guys. (Even granting that some of those guys were near free agency and that Ramirez wasn't Littlefield's fault, that's awful.)
(The same Primer poster also points out this irony - SI claims that the Pirates' poor performance isn't Littlefield's fault, it's the payroll - and yet it spends most of the rest of the two-part article praising Billy Beane.)