This is acknowledged in the book, which admits that not all Lemurians are sadistic psychopaths, and quite a few of them are decent people. On the other hand, they are delusional, and believing absurdities leads to committing atrocities. It does not help that the Lemurian worldviews are profoundly anti-human, viewing mortals as resources, problems, or enemies, or that Lemuria as a whole is schizophrenic. One day, a Lemurian might sell you 20kg of plutonium, the next, his boss sends 6 men with spiders for hands to kill everyone you love.
Chejop Kejak, leader of the Sidereal Bronze Faction in Exalted. He masterminded the Usurpation, an event which wiped out the Solar Exalted and ended the Age of Dreams, because the alternative was to take a very risky path to redeem the Solars that would, in all probability, have led to the destruction of Creation. Unfortunately, the side effects of the destruction led to the creation of the Deathlords and the Great Contagion, and Creation only survived the backlash by sheer dumb luck and a foulup on a Deathlord's part; the fallout from that event and Kejak's emergency responses led to the creation of the modern Realm, a corrupt dynasty of Dragon-Blooded nobility far degraded from even the Shogunate. To make things worse, Kejak has developed into a Knight Templar, constitutionally incapable of re-evaluating his standing agenda in light of the current situation. To be fair, that's the effect that the Great Curse has on all Sidereals, IIRC: to be completely unable to see any flaws in their primary motivation, whatever that may be.
As one friend put it, the greatest manifestation of the Great Curse was not any Solar jerkassitude (even Desus, he might just be evil, after all), but the life of Chejop Kejak.
Also, Abyssals 2e reveals that the creation of the Deathlords is the fault of the Gold Faction, not the Bronze: if they hadn't gone into the underworld and stirred up the memories of powerful Solar ghosts while trying to dig up secret information on the Bronze faction, the Neverborn might never have scented opportunity. So Kejak's sole contribution to the creation of the Deathlords was to inspire the people who didn't like him to do something epically stupid in the process of trying to shank him.
To rephrase Kejak's actions' motivation and their consequences, Kejak acted as he did in order to save the world. As a result of his actions, the world has died by inches, growing less glorious and closer to destruction with each cataclysm (until the present, when it's getting glorious again but seems more doomed than ever). And he can't see, much less admit, that he's wrong. Perhaps the inevitable result of playing it safe in a setting that runs on the Rule of Cool taken to Serial Escalation.
Strahd von Zarovich, seminal villain of the RavenloftDungeons & Dragons setting, flirts with the Anti-Villain trope from time to time, particularly where his past history as a war-hero and his steadfast defense of Barovia from outsiders is concerned. The rest of his past history, together with the fact that he's a vampire defending his larder, keeps him from slipping into it entirely.
Not quite on the nail there; the Emperor wanted the Space Wolves to bring Magnus (peacefully, unless Magnus disobeyed) to him to stand trial for his horrible crime he committed (inadvertently breaking the wards that the Emperor had set up to protect Terra from an all-out demonic invasion of Terra through the Human Webway that the Emperor had secretly been working on, simultaneously destroying the project, which would have permanently united humanity when completed. Magnus broke the wards by using forbidden sorcery to deliver the message, and accepted power from Tzeentch to break through the wards protecting Terra, when he was unable to do so... not quite "in the right" for his actions). It was Horus who, by this point already corrupted by Chaos, ordered Leman Russ to invade and destroy Prospero instead. Though Magnus did not know that it was Horus who ordered the Fall of Prospero.
The change was that it stopped being "let's become evil sorcerors", instead, he made a pact with Tzeentch to save his legion from extermination and it blew up in his face, killed everyone on his homeworld, and started Ahriman on the path that lead to the creation of The Rubrick.
Speaking of which Ahriman himself very much also qualifies, both in the creation of the Rubric which he intended to use to save his brothers, and his quest for the Black Library which he intends to use to attain godhood so he can free his legion from Tzeentch's control.
Alpharius could also be this. He had a secret meeting with the Cabal, who told him that the only way to destroy chaos permanently was to make sure that Horus would win.
When it comes to Warhammer 40,000, Cypher is the absolute personification of this trope. His goal is possibly the most noble and true goal imaginable: to reforge the sword he stole from the Dark Angels in his youth, and present it to the Emperor to atone for his considerable sins, which he knows will likely lead to his death. But because of the things he's done, it's impossible for him to go about it in any way resembling "good". Everyone in the galaxy sees him as a villain, he's infamous. But he's desperately trying not to be.
Nearly all Ogryns believe that all of their orders come from the Emperor Himself, being worked down through the chain of command. The forces of Chaos tragically exploited their child-like naivete during the Horus Heresy, with Ogryn handlers turning to Chaos and then misleading their Ogryns. Thus, many Ogryns waged war against Loyalist forces believing that they were still fighting for the Emperor and the Imperium.
The Eldar are usually this when presented as antagonists. They want to save the lives of their people. It's just that they don't care how many of your people's lives they have to sacrifice to do it.
Magic: The Gathering: Among the praetors of New Phyrexia, Urabrask the Hidden qualifies. His faction, the Quiet Furnace, is empowered by Red mana, the mana that embodies passion and emotion. As such he is not entirely bound by Phyrexia's will. Most significantly, Urabrask is capable of feeling compassion. When the Mirran refugees entered his territory, his orders stunned his followers and the refugees alike:
Deceiver Excrucians in Nobilis love the entire world...it's just that the thing they love is underneath layers of perceived "lies" such as up, down, fish, arms, legs, life and death. One of the metaphors given in their third edition sourcebook is that of a guy watching a friend hang with an abusive lover, except that that abusive boyfriend is the entirety of existence.