In Xiaolin Showdown fic Demon Of Wind, while Rai did choose to become Wuya's apprentice and is not without flaws, it's made pretty clear in the story that he never had any personal grudge against Dashi or his students and infact by the time he was finally turned to stone he was only staying with the Heylin side because he had to.
The LaFish brothers were paid off by Diamond Tiara to attack Pip and Soarin' during the Pegalathon, but claim it's Nothing Personal.
According to Word of God, Otto Bomb is only working for Professor Destiny (and Doctor Insanity) because the pay is good. He eventually gets tired of their suicidal stubbornness, and abandons them to continue the Pegathalon on their own.
In Fate:Zero Sense, Kirei and Wade manage to be this andCard Carrying Villains at the same time. While they are both unrepentantly evil, they also work for the author and follow his orders and when not being evil or breaking the Fourth Wall they live rather normal lives.
In Spiderman fic Polarity, Herman Schultz the Shocker is portrayed as this, openly admitting that he's only into crime because it gives him good pay and lets him be his own boss. As Boomerang eventually analyses him, and several other characters, villain and hero alike, agree, he's also a crook for the fame. He immediately goes to the aid of a woman who is being attacked by what he thinks is an attempted rapist at the story's start, and then, when a news channel shows a group of survivors being trapped by zombies in a nearby 7-11, he immediately gets his things and goes to rescue them, which he explains several times throughout the fic as being because the thought of leaving them to die like that, when he could do something to help, was just appalling. At the fanfic's end he joins the Avengers in the new world created by the end of the Zombie Apocalypse.
Yu-Gi-Oh! The Thousand Year Door has Lord Crump, most of the time. He is a suck-up to the Queen, but the only time he ever seems truly malicious towards anyone is when under the influence of the potion of bravery.
Discord's little sister, Rancor, in the Dark World Arc. She only becomes one of his Co-Dragons because Their Parents ordered her to do so and when its not her turn to fight the heroes is a Friendly Enemy, complimenting them and even helping undo some of the Valeyard's damage by giving Apple Pie the ending of the comic (revealing it had a Bittersweet Ending instead of a Downer Ending) he used as part of his efforts to Break the Cutie. As far as she's concerned, its Nothing Personal. In fact, when she finishes her mission (stealing Destruction's power back from Discord, mortally wounding him in the process), she opens a portal, tells the heroes goodbye, and leaves to do her real job as an Anthropomorphic Personification.
General Hercules Beetle from the Wedding Arc also counts. Despite being the second most dangerous changeling on the planet and having Undying Loyalty to his Queen, he's ultimately just a soldier doing his job. He's well aware that the Changeling's Fantastic Racism towards other species is horseapples and never shows any sadism or needless cruelty towards them, even being very respectful when not fighting. When it's not his turn to fight, he's content to just watch the ponies and learn about them. After being defeated, he's a Graceful Loser and suggests his former opponents fall back before reinforcements arrive. Really, the only reason Hercules is a villain is because his queen is evil and the moment she's defeated and replaced by Cadence, Hercules becomes a good guy as well.
Chef Hatchet in The Legend of Total Drama Island does his job (which frequently involves making the contestants' lives more difficult) in a conscientious and workmanlike fashion, but he'll also help the contestants out from time to time if it doesn’t conflict with his duties. He agrees to conduct the funeral service when Chris can't be bothered, and his attitude toward Sadie after her ordeal during the camping challenge could even be seen as kindly.
The Acolytes of Pein, from Naruto fanfic A Growing Affection, don't particularly like what they are doing, or what it does to Nagato, but they are unflinchingly loyal to him.
In the Babylon 5 fanfic Order In Chaos, some Drazi factions: they start the Centauri-Orieni War on the side of the Orieni, but stop any serious offensive after getting their asses handed to them by the Centauri, and when the Centauri Republic starts hiring mercenaries to fight the Orieni, many Drazi (often survivors of the early battles against the Centauri themselves) answer the call. At the same time, other Drazi (sometimes from the same faction) continue picking minor fights with the Centauri (and get their asses handed to them) for almost the entire war. Not surprisingly, the Centauri consider them Psychos for Hire and use them as cannon fodder.
Dig Build Live features the mobs of Minecraft sometimes being shown doing things on their own time, like watching films together, telling their kid a bedtime story, or even helping their own cross a railroad track.
In Vinyl and Octavia Duel Destiny, Prosecutor Milise Deauxnim is definitely this. Sure, he's a bit of a jerk who ends up getting both Vinyl and Octavia put in jail, but he's only doing the job he was hired for, and everything he does and points out is entirely legal/true.
In Origin Story, the various SHIELD agents, most especially Agent Dunne (who was completely honest with Alex and seemed genuinely upset that she was going to be imprisoned). Agent Dunne is also the only one to try talking Alex down before resorting to violence.
While a great deal of Gato's mercenaries in A Drop of Poison leave after their boss' death, several of them stay and get jobs around the village, including in the newly created police force the Torasen (which is otherwise comprised of Naruto's shadow clones). The clone leader of the group notes most of those who joined the Torasen were either Ronin or simply those who "left home to learn to fight, drunk on romantic tales of samurai life".
Captain Boomerang of the Royal Boo Guard in Can A Boo Be Friends With A Human isn't so overly enamoured with King Boo and would rather resort to diplomacy than fighting. But he can't leave when he has his family to be concerned about.
Stormtroopers in The Shadow might be harsh with prisoners and working for The Empire but they're not personally malicious. One of Luke's former prison guards invites him to the troops' weekly sabbac game after Luke becomes Vader's apprentice. He also rather likes Luke's nickname of him, Crank, as everyone else calls him ED-8 and "there's lots of Eds" and confesses that he joined the military because it let him leave his homeworld.
Black Three, one of Vader's personal wingmen, is a remarkably friendly young woman who takes Luke out for a burger once and regularly lets him borrow her speeder.
In Pinkie Tales: Cindershy, has Pinkie herself, as she plays one of the wicked sisters and has to be nasty to Cindershy, while being fully aware that she is only doing this because it is her role in the story and later goes through the fourth wall to help Apple Godmother make Cindershy a dress, when she was failing miserably.