One question comes to mind when I read this thread.
Do the prisoners deserve to live?
This is generally easy to evaluate. If they don't deserve to live (i.e. remorseless serial killers), then you execute them. If the moral ambiguity isn't there for the party, then they should just decapitate the prisoners. I don't see a problem with good characters eradicating evil in this way. If the legitimate governing power is just letting evil people go, then you should just kill them discreetly. I agree with Selgard, if the system doesn't work, it's time to be heroic and work out of the system. Let those chaotic good players be chaotic. They're still good. They should be trying to stop evil (mostly). Who cares if it's against the law?
As an aside, I imagine my current CG Magus character singing a rather controversial NWA song about law enforcement.