It takes more than just the person being Evil to make killing a good act- or even a nonevil act for that matter. "Murder" is defined as Evil in BoVD and Fiendish Codex 2- and there are plenty of ways in which killing an Evil person can qualify as murder- if there's not other justifying factors.
Other justifying factors might include "Self-Defence" or "Defence of Others".
Some acts might qualify as "always Evil" regardless of the context, like "Harming or Destroying Souls" or possibly "Torture" or "Using Evil Magic".
Though even here, there will be a scale- with "using Evil Magic" being very minor and "inflicting indescribable torture" being very major, in FC2.