Nava has been hitting like Goins this year. (.149/.240/.269). And with Victorino returning and Jackie Bradley Jr. establishing himself in CF, Boston could no longer afford to carry Nava on the roster, especially with the team 9-12, with several regulars regressing significantly. And trading Mike Carp is a non-starter.
Nava is actually hurting the Red Sox, with a -0.4 WAR this year. Of course, outside of the bullpen and Mike Napoli, the team is struggling as a whole. Defensively, they're below replacement level (-0.3 dWAR), with their entire starting outfield not named Jackie Bradley Jr. being below average defensively.