This article on Orcs and Goblins over on Silver Blade Adventures got me thinking more about the origins of humanoids. He suggests the idea - not new - that orcs and hobgoblins and such could be created by spells or bred in vats of broiling flesh. Dwimmermount takes a similar approach.
In my own game, the issue of "What about the children?" came up immediately as I ran B2 The Keep on the Borderlands. In that, you can see that my players spared the women and kids, and that I kept the "Gygaxian Naturalism" approach that meant that orcs, et al. are effectively just uncivilized but living beings. Wildmen, perhaps, but not inhuman monsters exactly. It feels cruel and un-fun to murder the kids, and you lose some of that "mythical humanoid creatures" bit.
I realized there is a sort-of middle ground. Perhaps orcs and hobgoblins, etc. are created monsters, either bred out of bizarre stock, warped from humans or elves, or built and shaped out of pots of boiled-down flesh and given souls by evil spells or unsavory rituals. Something like this is found in Robert Conley's excellent Magestic Wilderlands supplement. If that's how they originate, they can easily be conceived of as pure evil.
But what if they breed true? What if they're still initially bred (and can be bred) in those bubbling vats or formed with evil spells, but the males and females can create young that are equally as evil as themselves?
They become more like a self-replicating demonic virus than just another race. The kids must be expunged, because they're simply going to make more of this nasty race. It's like picking weeds or wiping out termites to kill them off - you need to get the whole lot or the problem isn't solved.
This does have the downside of making half-orcs a bit harder to justify. Or perhaps making their reputation as boors and assassins more justified - they're bred from evil, even if, like Merlin, they turn that demonic taint to good ends.
But it's got the potential to split that Gordian Knot of "I want orcs with mythic origins but I want to preserve the Gygaxian naturalism of female humanoids and kids." Or "I want the have orc women and kids but not have my Paladin get smote down with lightning for killing one."
As for my game, I'm not telling the origins of my races just yet. My players read this blog. But it's worth noting that there is still a tactical reason in my games to spare the women and kids - it makes the humanoids easier to bargain with. My players are after loot, so if sparing a few weeds means the garden yields up its veggies with less work, well . . .