The right thing to do and the best thing to do are sometimes mutually-exclusive; when Fluttershy finds the deposed Chrysalis injured and near-death in the Everfree Forest, she knows that the wisest course of action to pursue would be to leave her to her fate. She's a sworn enemy of ponykind, after all, and will only seek to hurt them further once she's rehabilitated.

One's true nature can never be changed, can it?