My understanding was that they thought they were signing up with SHIELD and didn't know it was HYDRA until later (when everyone else found out?), and I'm also going to guess that even if she's had the powers for a while, she was only able to control them for a much shorter period of time, and so couldn't know if what she was seeing in their minds was everyone or a few bad apples or what. And that's without knowing whether they were being kept in a place that had some sort of shielding (while Magneto doesn't exist and isn't their father here, I wouldn't be surprised to find that similar technology to his anti-telepathy helmet exists in the MCU).