I agree, and the JD pull was questionable, but I think without the benefit of hindsight, Cora probably expected this...
1) A better chance to score with a faster runner, and it almost worked.
2) Better late inning OF defense with Holt moving to LF after the move. (I'd have tried to work it out where Beni stays in the game not Kinsler.)
3) He did not expect 18 innings and 3 more PAs from JD's slot. Nobody figured that.
4) JD running the bases increased the odds of tweaking the ankle.
I'm not saying I liked the move, but there were several reasons on the plus side, but hindsight shot down some of them.