I don't think the organization "has done Danks wrong," but I do think the organization - with it's emphasis on longevity and profit over performance excellence - often prefers veteran mediocrity over young mediocrity.
In this exact situation, I'd keep Wise over Danks because Danks has options. But I'd look for a way to get a player better than Wise.
Actually, let's think big picture. I'd look for a much better starting CF, to push DeAza to the bench and push Wise and Wells off the roster.
The universe is the practical joke of the General at the expense of the Particular, quoth Frater Perdurabo, and laughed. The disciples nearest him wept, seeing the Universal Sorrow. Others laughed, seeing the Universal Joke. Others wept. Others laughed. Others wept because they couldn't see the Joke, and others laughed lest they should be thought not to see the Joke. But though FRATER laughed openly, he wept secretly; and really he neither laughed nor wept. Nor did he mean what he said.