Yeah basically you answered one of the questions. To you killing an evildoer is a good act and killing an innocent is an evil act. Some would argue the action of killing another person is evil in itself no matter the reason.
When they were discussing it Satsuki asked if they were against beating Alice up, and they werent. As far as that goes it's fine, but by our modern world's morality they really should've captured and brought her to justice rather than killing her there, and doing so kept relatives of other victims from seeing closure as she was never formally punished for the other murders.
To be clear, the part that is more ambiguous here is Will and co's actions rather than Alice's, and not second guessing your actions is how one ends up like Alice. She believed she was good and doing something for the good of the world and everything was a necessary sacrifice for it.
