All the enemies are dead except the boss who says he surrenders, what do you do?

[Quertus]

This is all aside that you are trying to force the necessity for good aligned people to need to a reason to not kill people, when it should be the other way around, that good people should need a reason to kill people. In the outlined scenario, the reason to kill the minions is that they are actively trying to kill you and that you can't safely subdue them. The reasoning for not killing the surrendering leader is then a rather obvious: He is not trying to actively kill you.

That's exactly the warped version of "good" I was talking about: the minions trying to kill you is reason to make them killing you not happen; however, "killing them" is not a prerequisite for them to not kill you, particularly when knocking them out instead is, as others have explained, quite non-lethal in 3e. So "they're trying to kill you" is a reasonable Neutral reason to kill someone; Good should look at more details than that. Otherwise, we're just in "team jerseys" territory, where everyone is trying to kill everyone else with a different jersey color, simply because those with a different jersey color are trying to kill them.

This ability to incapacitate the minions does, of course, open up the option for an as-yet unexplored path: not killing all the minions, then killing the surrendering leader (rejecting their surrender, or accepting their surrender and then executing them for their crimes). Although this is perhaps the most likely path that one of my Good characters would default to in a "bandits" scenario, it is not an option in your more specific "bandits where you've already killed all the minions" scenario.

But I don't play Good characters very often anymore. Most of my Good characters are dead. I'm batting for team Lawful Evil these days.

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What would my characters do in this scenario?

Quertus: Well, the Bandit Leader attempting to surrender is kinda... odd. Because Quertus probably nuked the site from orbit. (perhaps the bandits stole something he had shipped in; annoyed, Quertus (performed divinations, scryed through time, then) teleported through space and time, and replaced the shipment with, well, something that went "boom" (for example, a few hundred metamagic'd Delayed Blast Fireball gems stored in Quintessence, plus a few diminutive Simulacra to extract the gems at the appropriate time)). Or he sent an army of Golems to deal with the problem. In any event, in the strange scenario where my epic wizard was dealing with bandits, their calls for surrender should go unheard. On the off chance he was somehow "on the ground" dealing with bandits (they happened to be camped at the site of a rare convergence of magical energies or something, and they mistook Quertus for an adventurer come to wipe them out, and attacked), calls of "I surrender" would, perhaps, be met with a response of, "don't resist", followed by Quertus casting a spell (most likely Polymorph Any Object, to turn the surrendered leader into a shovel, or whatever other tool Quertus thought he needed at the moment).

Armus: Armus most likely hired the bandit leader (likely through an alias), to manipulate the political landscape (and/or, in the case where we've killed all the bandits, to collect irredeemable ne'er-do-wells in one place for the party Paladin to slaughter), so of course Armus would (say what was necessary to get the party to) accept his pawn's surrender (unless getting the pawn killed was somehow part of the plan).

Illirian: The only reasons Illirian wouldn't pull a Stark and execute the surrendered bandit leader would be if someone else had greater claim to swing the blade, or if the party didn't accept the surrender and killed the bandit leader outright.

Briq: Yeah, um, Briq would beat the bandit leader unconscious, just as he did to all of the minions that he came across. Apparently, someone else in the party has been going along slitting all their throats after the fact (probably the paladin), and I expect that they'll do the same to the bandit leader.

Eladove: Nah, she doesn't need a bandit leader (A'Jin: especially an unnamed NPC) as a Synthesis - they need to at least measure up to Hessalo Synthesis One, Irmutar Synthesis Two, and Rathkuul Synthesis Three.

Pidge: Pidge would disarm the bandit leader - literally, as in remove his arms. And his tongue. And eyes. And all his hair (including eye lashes, eye brows, etc) and teeth. And wonder if he missed anything. Which leads us to...

Delock: Much more efficiently, Delock would simply turn the bandit leader into a brain in a jar. We can always give him a body back later if he is absolved of his crimes.

Anna: <Bang!> <Headshot!> "Sorry, what was that?" Much like Quertus, Anna would not be in range to hear the surrender; unlike Quertus, she isn't terribly perceptive in the first place.

Rita: (looks for a Staff of the Magi to break across the bandit leader's face)

Datch: "Finally, someone who surrenders! ... Don't resist" <Arcane energies>

Korin: "Sorry, I've ordered too many undead to kill you - I can't order them all to stop in time. So make peace with whatever gods you follow - quickly." (turns to party) "Can you believe I used to be good, and that this used to be something of a moral dilemma for me?"

K'Tamair: K'Tamair am be taking bandit leader's belt, am be tying their shoe laces together.

Raymond: (Quirks an eyebrow, turns to party/Tivek) "Is he worth keeping?"

Tivek: (looks bandit leader over) "...Yes. Let's invite him to dinner."