The TU has a goal that everyone can agree is worthwhile, and there's at least some hope that the plan might work. However, this particular road to utopia is Powered by a Forsaken Child or simply includes a nauseating level of necessary sacrifices.
Well, if people are allowed to do whatever they want, they'll make a mess of our Utopia. Better get rid of that pesky free will.
The problem is the analysis
The TU has a good goal, but while their means may seem okay (to them, at least) it has hidden/'hidden' costs. Even if the plan does solve the original problem, it will only bring about something even worse. For example, they may try to prevent crime by sacrificing everyone's souls to an eldritch abomination so they will no longer have personalities or feel the desire to steal. They may not have even realized that this is a problem.
The problem is the goal
The TU is off the deep end. Their idea of 'the greater good' is simply wrong and/or may suffer from a heavy dose of Insane Troll Logic. Any principle, no matter how reasonable it is if paired with common sense, can become Nightmare Fuel if you take it too far... For example:
We should maximize the average happiness. This can be done with 'exiling' (and then secretly exterminating) the unhappy people.
Negative Utilitarianism: Instead of maximizing happiness, we should only focus on minimizing suffering. However, since all living things suffer to some extent, we can only eliminate suffering by putting the unhappy out of their misery.
In Psycho Pass the Sybil System and the people who work to keep it in control of society are this, with the anime starting AFTER they succeed in realizing their goal. Near the midpoint of the show the idea of maximum happiness is highlighted as why the system is so great. All it asks is that you submit to it deciding your entire lifepath, constant drone overwatch, the threat of permanent detention or even execution if the prediction system decides you might commit a crime, and the further threat of constant mind-altering drug applications or detention if you have a chronically negative mood.
Light Yagami of Death Note begins here with his plan to make the world a better place by systematically killing all its criminals, starting with the world's worst offenders and ending with those who merely aren't living up to his standards, but swiftly veers off course into wanting to become "the god of a new world."
GUN×SWORD: The Claw and his minions are this all the way, being mostly the nicest people you can meet, and who want to bring about a better world through an Assimilation Plot, and will kill when necessary to achieve this goal. Notably, the heroes are generally very individualistic and less personally pleasant, and it's suggested that the Claw's plan probably would bring about a better world if successful.
Code Geass: Charles di Britannia and Schneizel el Britannia, full stop. Lelouch can also be considered this when he engages the Zero Requiem, considering there are less bloody ways towards world peace, but is at worst a Woobie, Destroyer of Worlds considering what has happened to him, and his intended end result.
Kyubey of Puella Magi Madoka Magica is trying to stave off the heat death of the universe. By dooming teenage girls to lives of suffering, and killing plenty of innocents (potentially entire planets) along the way. The primary problem here is that there's trillions of years to come up with a less terrible plan.
Gretchen Kriemhild, Madoka's witch form, is a negative utilitarian. Whereas Madoka cares deeply about making everyone happy through positive means, Gretchen wants to erase suffering by assimilating each and every sentient being into herself, which is a Lotus-Eater Machine.
Speaking of |Erase Humans -> Erase Suffering| logic, the girlfriend of the evil priest in Book of Bantorra has developed this philosophy, due to being imprisoned within the priest's soul for ages along with the souls of thousands, if not millions or billions, who have been stuck in the purgatory of existing in a allegoral plantless desert. This turns her into the big bad, Woobie, Destroyer of Worlds type, and forces EVERYONE ELSE (who isn't a monster or too tired to exist) to participate in the fight for Book-Earth.
The Pro-registration side in Civil War turned out to be this. The goal? Insert some accountability into superheroics. The means? Creating an insane clone of Thor, imprisonment without trial in a hellish extradimensional prison for anyone people who didn't go along with it, granting functional pardons and extra powers to supervillains, notably putting NormanOsborn in charge of a government agency, and the conscription at gunpoint of teenagers with superpowers.
Osborn himself qualifies, at least in his own mind. He thinks that the superhero community is likely to usher in The End of the World as We Know It and wants to save the earth — too bad he's a psychotic superhuman himself and far more dangerous than any of the people he's opposing.
The Big Bad of Watchmen, whose goal is to end the Cold War and then use his abilities to control the Earth and make it a paradise on Earth. His problem is mainly a type 1, killing half of New York in a Genghis Gambit, but the ending implies it may also be a type 2, assuming naively that this is all that is required to defuse a 40+ year old nuclear standstill and failing to take into account Rorschach's diary.
In Serenity there is the Alliance, which tried to create a more peaceful world through chemical testing leading to untold numbers of deaths and the creation of a breed of rampaging psychopath space pirate, and their hatchet man, the Operative. Notably, the Operative acknowledges that when they've built their "perfect" world, he won't have any place in it.
In Wild Swans many of the revolutionary communists are portrayed like this, while others are portrayed as Straw Hypocrites or simple cases of Peer Pressure Makes You Evil. The latter includes the main protagonist herself.
In the Discworld novel Witches Abroad, Genua is run like this. People failing to be happy enough (and stereotypical enough, as the ruler's goal is to make Genua a fairytale-esque city) are dealt with harshly.
There's one Stanislaw Lem story about a society which builds an Artificial Intelligence that has to create the perfect world. The AI does this by building a factory, taking people one by one there, with the promise of a happy place, and noone ever returns from there (that alone should ring some alarm bells, but apparently the people aren't Genre Savvy). Truth is, in the factory people are turned into shiny metal discs, which the AI later arranges in a geometrical pattern. Apparently it's a bit of a Literal Genie and didn't understand that this wasn't what people had in mind with "the perfect world".
He also plays with this in Eden, where any Edenite who isn't perfect is killed, and everybody's okay with this. Even though they've a rather high mutation rate. It should be noted where he lived and when.
Totalitarian Utilitarian is actually a common theme in Lem's stories. Experimenta Felicitologica would be another example.
The Lord Ruler of Mistborn tried his hardest to be this. Pity Ruin was in telepathic contact with him for his whole thousand-year reign, twisting his utopian vision into a postapocalyptic nightmare.
The society in The World Inside by Robert Silverberg is one in which people have decided that the best world is the one with the most people in it; the vast majority of the world's current population of 80 billion all live in giant, city-sized apartment buildings with no privacy, while all the rest of Earth's habitable land is devoted to agriculture. It is theorized that the maximum population that can be supported this way is 200 billion.
In Star Trek, the Hive Mind called The Borg seem to honestly believe that getting assimilated into their collective is the best for everyone.
The classic series Doctor Who episode, "The Happiness Patrol", tells of a society in which the tyrannical leader Helen A has all the "killjoys" - basically, anyone who shows any sort of unhappiness ever - killed, occasionally in bizarre ways. For bonus points, Helen A is also an obvious parody of then-Prime Minister Margaret Thatcher.
In Angel Season 4, Jasmine, essentially the Big Bad of the season, is an example of Type 1, wanting to bring pure happiness to the world by mind control that would have removed from everybody the free will to be evil. Whether the tradeoff would have been worth it can be debated.
Myth And Legend
In Classical Mythology, there's the Golden Age which is identified (at least in some versions) with the reign of Kronos. Now there was a prophecy that one of his children would topple him, like he had toppled his father Uranos. So Kronos ate all his children to avoid this. Not sure whether he did that for concern that the Golden Age should continue or just because he himself didn't want to lose power, but if it was the former, this would be a case.
Being unhappy is also a crime in Feng Shui's 2056 juncture, where everything is ruled by the Buro.
There's also the Jammers, who want to free the world and humanity from the "tyranny" of Chi by destroying all Feng Shui sites. Sites that often take the form of schools, hospitals and other places important to a community or where innocents tend to gather. And to make things worse, they haven't given much thought as to what will happen once all Chi and Feng Shui are destroyed, and what the consequences will be to the world — and given that Chi is said to be tied to life itself, the consequences could be very bad indeed.
In addition, one could interpret that the actions of the God-Emperor of man to be manifestations of this philosophy. His own philosophy appeared to be a form of "radical secular humanism". His goal was to ensure survival and security the human species, and it's mastery over the galaxy, and eventually the entire cosmos. He believed that this goal was best realized by causing humanity to accept science, logic, reason, and secular humanism, and reject superstition, mysticism, and any religion (or competing philosophy) of any kind. Therefore, in his mind, the best way to do this was to launch a "Great Crusade" to conquer the galaxy led by fanatically loyal genetically-engineered super-soldiers who would kill or convert any and all humans they encountered, as well as completely exterminate almost every non-human they encountered, which resulted in the deaths of countless sentients and the destruction of whole planets. He also lied about the existence and nature of the VERY-real demons and dark gods which do inhabit a sort-of "preternatural" plain of existence, and treated many of his direct offspring, the Primarchs, as mere tools to be used rather than as people. All of this in order to create a unified human civilization under his direct rule. And the ironic part? In the end, the vast majority of humans ended up worshipping him as the god of humanity.
In later BattleTech fiction, particularly the Capellan Solution duology, Sun-Tzu Liao is this trope. It's all about the good of the Capellan Confederation for him (as he sees it, of course), and no trick is too dirty or underhanded and no sacrifice too great if it brings him one step closer to making his nation great again.
In Mage: The Awakening, the Silver Ladder wants to restore the connection between Earth and the Supernal Realms, allowing all of humanity to achieve godhood. They end up doing a lot of shady manipulation and exploitation in their efforts to bring everybody into line with their plans and frequently end up falling into Ambition Is Evil by pursuing power for its own sake.
Sofia Lamb in BioShock 2. Her goal is to create a "utopia" by using ADAM and mind control to imbue everyone with the entire sum of the knowledge of Rapture's inhabitants, eliminate their free will and instruct them to act only for "the greater good" (pretty much turning everyone into mindless slaves). Starting with her own daughter.
Valmur of Suikoden Tierkreis is half this and half trying to survive. On the one hand, he believes there's no way to beat the One King, and that those who ally with it will be spared. On the other, he'd probably ally with the One King anyway—in return, he and everyone he follows will be placed in eternally repeatingillusions of the best days of their lives. To Valmur, who is unable to accept the deaths of his family, even an illusion of their return is better than reality, and he's willing to inflict the illusion on everyone else. Of note is that at least for the protagonists, it doesn't work—the gun expert grows weary of never completing his greatest design; the farmer realizes his crops will never be harvested; two lovers know they'll never be able to raise children . . .
Hell there's a message you can read in the DLC Lair of the Shadow Broker where a major asks for Admiral Hackett's permission to have Shepard arrested and interrogated for a few months on why s/he is working with Cerberus. Thankfully, Hackett denied that request.
Shepard him/herself can act in this way, especially as a renegade. Unlike in many games with a Karma Meter, renegade Shepard is still basically one of the good guys. Which essentially means that s/he can kick and gun down a great many canines, and defend various atrocities in the name of the greater good.
One 2010 arc of Sluggy Freelance centers around an Alternate Universe, 4U City, which is this sort of society. Happiness is enforced through a mandatory regimen of drugs, and anyone who shows signs of being the least bit morose is 'judged' (which basically consists of zapping them into a random alternate universe.)
Lord Doom from the Global Guardians PBEM Universe is dedicated to solving the world's problems and making the world a better place so no other child has to watch their family be systematically killed like he did during the Holocaust. To that end, he intends to overthrow every government on the planet and replace them with his own benevolent rule, modify the general behavior of the human race through genetic engineering, drug thereapy, and branwashing, end crime by ending the criminals, permanently, and insuring that the only people who have the capacity to make war are those who have been programmed to be loyal to the cause.