Morgan Fey loves her young daughter Pearl Fey. That's why she tries to let her be possessed by the spirit of a raging, vengeful serial killer. This one's confusing, since said raging, vengeful serial killer ghost is Morgan's older daughter.
Shelly de Killer keeping Maya hostage for blackmail for Phoenix to defend Shelly's client Matt Engarde.
Kristoph Gavin's attempted murder of a 12-year-old agoraphobic girl probably counts too.
Solid Snake (or rather, the player) in Metal Gear 2 is actually given the option of murdering orphaned war children in Zanzibar Land, and despite being raised in a soldier nation, apparently they don't have orders to attack Snake or sound an alert (they just seem to just give advice and talk to him), although it does result in his health going down. Also, in the (albeit non-canon) radio drama for Metal Gear Solid, Solid Snake and Mei Ling argue about whether there is a significant difference to killing child soldiers and regular soldiers. Solid Snake mentions that he doesn't see a difference, which indicates that he is not above killing child soldiers.
Return To Krondor: Played straight. In the first chapter, a ten year old girl who is a thief and an orphan living in the streets truly does not want to go to The Order of the Yellow Shield, a group that owns an orphanage. That is because men who pretend to be members of The Order of the Yellow Shield lure kids like her to a sweatshop. At this sweatshop, they work the kids hard, hurt them, lock them up in cages, as well as giving them food that have live rats and squirmy things in it. She also says about how the bad children (i.e. kids who refuse to work or try to run away) just disappear and never come back. Investigating the sweatshop reveals that everything she said is true. You will find a cage with kids locked in it, and depending on your decisions, you will find the bloody corpse of a child in one of the boxes next to the entrance door. James will be very unhappy with that discovery and refer to the owner of the sweatshop as a "child-killer". A camp of goblins sacrificed a boy, cutting him in two, and they were going to do the same to baby twin girls. Vampires killed and converted kids as well as adults to vampires. Ghouls are explicitly said to feast on human flesh - and that would include children. There is also a priest who is devoted to Sung the Pure named Father Roweland who is trying to help children recover from a fatal disease, but he causes the fatal "disease". He actually killed a little boy with evil spells, and was going to do the same to a little girl with an evil amulet magically disguised as a good amulet, as well as evil spells. A woodcutter, his wife and child disappear, but the woodcutter and his wife (not really his wife) sacrificed their child (not really his child) to try to power up a Nightstone. The Nightstone is found on a small skeleton, which could very well be the child's remains. Bear also used explosives to set an orphanage on fire while escaping Krondor - with the kids still in it.
Ditto Postal, at least until you pop in some unofficial mods for either series.
A side mission of Drakengard features Anti-Hero Caim slaughtering child-soldiers with about as much gusto as he slaughters everything else, i.e. a lot. The children run away and scream for their mothers as you cut them down, while Leonard and Red calls you a monster for it. And then there's that child-eating Elf cannibal he travels around with, and Leonard was originally a pedophile in the Japanese version... Yeah, Drakengard doesn't like children a whole lot.
And in Alternate Continuity sequel NieR, some of the shades that Nier slaughters are actually sentient children who cannot communicate with the "humans", particularly Kalil, the "boss" of the Junk Heap area.
The plot behind Heavy Rain centers around a serial killer that targets boys from the ages of 8-13. It makes replaying the Suicide Baby chapter much worse once you know who the killer is...
Anybody in the Kingdom Hearts universe will have no trouble with fighting the main characters, most of whom are teenagersnote Terra and (possibly) Aqua being the only playable characters over 17, so they have to take all their opponents seriously, so it's all fair play. Master Xehanort even manages to kill one of them (Sora) and steal the body of another (Terra), though the former gets revived.
Dragon Age: Origins is a rare game which lets a player character do this, as you can chose to murder Arl Eamon's son rather than try and help him. You might argue that it's a mercy-killing, but you're still killing a child.
The Human Noble origin has your character find their sister in-law and young nephew dead during the attack on the castle. By this point, it's clear the attackers don't care about hostages.
And we have this little gem right before the attack:
Mars and his soldiers in Tales of Phantasia. They kill everyone in Toltus, including Chester's little sister and a random girl whose corpse you can examine.
FunFrock in Little Big Adventure 2 initially uses kidnapped children in order to force the wizards to co-operate with his scheme. When Twinsen invades his lair, he decides to drop the children into a volcano in order to make Twinsen cross the Despair Event Horizon.
With all the little sisters running around pumped full of sweet, sweet ADAM, most Splicers will try to kill them if given the chance. Good thing the big daddies are there to protect them.
Also, the heartless bastard who put the girls in this situation is later killed by a big daddy after he slaps one of the little sisters who was irritating him.
BioShock Infinite: Daisy Fitzroy falls into this trope when she attempts to murder a young Founder child because, as she says, "the only way to stop them from growing is to pull them up from the roots!" This is enough to stir Elizabeth into impaling Fitzroy with a pair of scissors. However, Burial at Sea: Episode 2 reveals that Daisy was ordered to do so by the Luteces in order to strengthen Elizabeth's resolve by getting her to kill in order to set forth the events of Comstock's downfall and that she was actually horrified at the idea of killing Fink's son.
The first two Fallouts gave you the title Childkiller if you killed a childnote Well, at least two, which would cause almost everyone, even other renounced scumbags and lowlifes, to hate you. At least the children were scripted to flee when accidentally hit, so they rarely got killed by NPCs. In Fallout 2, once you've progressed through the game long enough in an attempt to go to another settlement, you'll get an encounter that shows an Enclave patrol coldly killing a small family, including an only child, which serves as an ominous Foreshadowing to their existence, who have no qualms in exterminating any being that isn't them or wasn't born in a Vault, and yes, that includes children. The Fallout 3 and Fallout: New Vegas had invincible children (unless you use some mods...there is even a very famous one which implied eating a baby in exchange for the benefit of a perk which give you rads immunity, you can see this marvelous sickness here)
In Fallout 3, the player can, however, enslave selected children NPCs and cause the implied deaths of two others, by blowing up a town with a nuke.
Fallout: New Vegas has two slaver traders making a note not to do any more business with the raider leader Cook Cook, as he burned a young boy they had sold to him to death. The player can also ask a prison rioter who goes by the nickname Scrambler what he was in for. He responds that he doesn't really care enough to keep track of his crimes, but he vaguely remembers something about killing a lot of people, and that some of them probably were kids.
Final Fantasy XIII has Hope Estheim - the youngest, most physically weak character in the game. That doesn't matter to anyone; he's a Pulse l'Cie, and therefore must die.
Before this, he and a town were put on a train, and promptly shot at by the military when they tried to escape.
All the protagonists in the Mother series are children (so obviously, plenty of the enemies that battle them will be adults), but perhaps the most notable specific example of this trope is in EarthBound when a bunch of policemen beat up Ness just because he wants to leave his hometown.
The Legend of Zelda: The Wind Waker has Ganondorf hitting Link, who is around 12 years old in this game, multiple times until he loses consciousness and has his sword knocked from his hand. Later, during the final battle, Ganondorf uses some very brutal and painful-looking sword moves against Link.
The Shroobs and their army in Mario & Luigi: Partners in Time seem perfectly willing to kill Baby Mario and Luigi after beating their adult selves. Kamek too, who's also technically guilty of this in Yoshi's Island and its sequels (he starts by attacking the Delivery Stork in the intro, then tries to get rid of the Mario Bros. by any means possible afterwards).
Mario and Luigi themselves when they fought Baby Bowser in Thwomp Volcano or when they fight Bowser Jr. in the mainstream games. Mario also fought Jr. Troopa in the original Paper Mario, although the kid kind of has it coming for constantly harassing Mario and challenging him to fights all just because Mario and Goompa accidentally wandered into his playground.
Metro Last Light has its fair share of children dying or dead. Most notable examples are the bombs that forced people down into the Metro, as well as the synthetic Ebola epidemic that Korbut released on the neutral stations that takes out every man, woman and child there- not to mention the executioner mop-up crews that are sent in to set the place ablaze and kill absolutely everybody.
Baldur's Gate has the gnome Jeb, who enjoys murdering street children. Unfortunately, you have to make allies with him in the first game in order to escape from prison; in the second game, however, you encouter him again, and can give him what he deserves.
In Crusader Kings, not only is assassinating children possible, it even comes with special text to fit. It's often a simple, if brutal, way to clear up the line of succession so one's own character can inherit.
Skull Girls: Black Dahlia, the Medici mafia's top assassin did not even hesitate to put a bullet through the head of fourteen year old Sienna Continello and actually taunted the poor girl's mother while doing it. She also threatens to kill the also fourteen year old Peacock in the latter's ending, but in that case it is more justified as Peacockhad been slaughtering her way through the Medici stronghold up to this point.