It doesn't take too many instances of "You know that evil Cultist/Necromancer/Whatever you let go last month with a promise he'd quit his evil ways? Well, he didn't and he's BACK!" before prisoners simply get the sword.
This is where action resolution mechanics seem apposite.how the GM chooses to “reward” this decision also goes a long way. As mentioned earlier in the thread, if every prisoner released comes back to cause trouble for the PCs, they’re going to learn a specific lesson. So the GM needs to decide what he’s looking for in the game, and then make sure to proceed accordingly.
If the PCs release a prisoner on his/he parole, and then that prisoner breaks his/her word, that is clearly a failure. So should be the consequence of a failed action declaration. Whereas if the players succeed in their action declaration then the GM should honour that, and have the NPC keep his/her word.
Different RPG systems have different ways for adjudicating this, and depending on broader feature of tone and style it might be more or less cynical or light-hearted. Even within a given system there might be different ways of doing it - eg in Classic Traveller repent or else seems like it might be resolved via a morale check, whereas why don't you come over to our side seems like it might be resolved via a reaction roll.
But if a GM repeatedly, unilaterally turns player successes - we beat the bad guys -into player failures - the bad guys we released on a promise of good behaviour have gone back to their old ways - then (i) that sounds to me like a bad play experience, and (iii) the players will start taking steps to impose finality on the fiction, as the only way to try and control the GM. Killing prisoners will be one form such finality takes.