I speculated at the time that the trade was compensation for Benedict, because it made no sense on its face. Williams was the Marlins' fifth-ranked prospect (in a horribly depleted farm system, but still), and he's close to the majors; Mitchell, meanwhile, was a million miles from the majors and wasn't that likely to ever get there. Stark notes that scouts say Mitchell is a "non-prospect."
Stark writes that the Pirates were reluctant to let Benedict leave for Miami, since they had him under contract and since the Marlins had already recently hired another former Pirates special assistant, Marc DelPiano. Apparently, within in the industry, it's common practice not to let more than one executive be hired away by the same team.
Anyway, that solves that mystery. Williams doesn't appear to have a ton of upside, but he can start, has experience in the high minors and isn't even on a 40-man roster yet, so he should give the Pirates some flexibility over the next few years. Benedict was a tough loss, but at least the Pirates got something in return.