If she felt guilty, why did she commit the same crime with Agatha before leaving town? She took away a person's free will and didn't blink.
Because unlike the rest of the town, Agatha was a direct threat. She'd already seen memories of Agathas and Agatha straight said that she goes around absorbing magic from other people. Even if she was feeling guilty, she still had to make sure Agatha couldn't do that again to anyone else. That means she had two real options, the first being to outright kill her while she was defenseless, the second to be what she did. Maybe killing her would have been a mercy, but they're not about to have ostensibly leading heroes in the MCU murdering in cold blood.