It really depends on where you are within the AP and where the characters are physically. If it is near civilization then fairly easy to do manacle them up and send them to trial.
Ultimately it is an amazing roleplaying potential point to see how the players react.
As for killing the prisoner to be an evil act, if they are judged and guilty then the LG has to options. Try to redeem them or execute them according to the law and go all Edard Stark and do it themselves. I'm so looking forward to these scenarios.
From a Pally perspective, really cold blood killings are only going to twitch the alignment meter on the fully helpless non-guilty. Kill the rampaging orcs but you find nearby a group of orc children, and you go all Anakin on them. Yeah, that's a slip.