It read a lot to me like she is working for someone else. Almost certainly not Hydra. But I seem to recall that the comics had a variety of post-shield shield variants at one point. She was, after all, very strongly sounding out coulson to see if he was like Fury; it is plausible she is a triple agent. And that could have been something Mack and Hartley (Because Mack as much as says Hartley knew about whatever it was) knew, and Mack wanted to see if she wanted to flip hunter.