She may not have liked her at first, but she was sad to see her go.
And they could tell Echo was disappointed they had to leave as well.
Asclepius had informed them on the cure to Echo's noiselessness, the only way possible to lift the curse of a god. But the secret behind the remedy wasn't something they were willing to embark on, especially when the girl they would do it for wasn't all that close to them. It was too risky. Too dangerous for them. As heartless as it sounded, they had no other choice but to abandon her. They didn't know Jack all that well either, but they were responsible for the harm that had befallen him as well as the destruction of his home. The way they saw it, they had to help Jack above anything else.