For some reason I actually can't remember how she came into custody of Garrett. Or what was said in terms of her knowledge. But I suppose what you say is possible. But didn't she think Coulson was Hydra? She was bringing The Bus back on auto pilot and not trying to shoot it down. Perhaps because she wanted to find out the alliance of the rest of the team? But then again, she would have known the drones were shot down and Garrett's plane docked with The Bus. If "knowing" Garrett was Hydra and at least suspecting Coulson (IIRC) were Hydra would she have still brought The Bus in? Or shot it down team and all?
Sorry, just thinking out loud folks. Jedi business, go back to your drinks.
I believe Hand wanted the Bus for the info stored on it, so they couldn't destroy it.