"I'm sorry that you both had to suffer like that," Sydney said sympathetically even though she didn't know the specifics of what River endured. It didn't matter what they did if it was enough to send Simon and his sister on the run and make him turn to a life of crime to protect her. "Sometimes organizations that think they are operating in the best interests of others are the ones we need to be most skeptical of."
Her experiences with the Alchemists after her adventures with Rose gave her a healthy dose of skepticism and paranoia with regards to their practices. It wasn't anything she was comfortable voicing or even really thinking, but here, so far removed from it, she had to acknowledge it was true.