"Every time I leave these sharp knives out, people cut themselves, so from now on, I will put the knives in a secure place, and only allow knives to a select few individuals I deem trustworthy. Their un-regulated use results in negative outcomes a lot, so I'll keep them someplace secure, and if someone wants to use a knife, they can come to me and I'll decide if they can be trusted to use them wisely."
Malygos had mortals join him, and allowed them use of magic. He hoarded magic and allowed people to use it if they understood that he'd have his eye on them and wouldn't let them abuse it to the point of catastrophe.
Unlike most characters in the Warcraft universe, Malygos put his duty over his own personal vendettas.
It's one example of what happens when just anyone can tap into magic and use it for whatever they want, whenever they want. Malygos couldn't just pick and choose who could use magic and who couldn't. If some mortals were going to use it for purposes that would result in cataclysmic outcomes, then he thought for the greater good, it must be taken away from everyone, except his own mage-hunter collaborators who joined him at the Nexus.
Yes, because now they know about the titan soul, and they know that Azeroth is not destroyed. The humans' reckless use of magic was what tipped them off. Yes, the Council of Tirisfal worked until Aegwynn, that's not in question. The problem is that they just slapped a bandaid solution on, rather than try to fix the problem at its source: the fact that they were practically waving a big sign and shouting through a bullhorn through the Twisting Nether saying "HEY, BURNING LEGION, WE'RE STILL HERE AND STILL HAVE MAGIC, COME AND GET US!!!"
If they hadn't been shining the Legion-equivalent of the Bat-Signal into the Twisting Nether sky, the Legion would never have returned.
How many bad eggs would you accept before you concluded that the group was just too unpredictable, and you couldn't predict who would cause problems and who would be fine? To Malygos, they're all just foolish mortals with no mind for caution or responsibility.
If you can't possibly prevent the catastrophic disasters while the people have free access to magic, then the logical course of action is to take the magic away, and then dole it out only to those you deem trustworthy.
Wasn't saying it didn't concern them, just that the Kirin Tor is reckless and leaps before they look, jumping into Northrend and then being like "oh no, looks like we bit off more than we could chew, so let's send someone crawling to the Blood Elves for help because Quel'thalas is always our go-to whenever we're in a bind and need a favor we'll never repay or take into account the next time someone accuses them of treachery and we all immediately believe and are happy to slaughter and imprison them."
Too bad Blizzard has forgotten that you need to convince the player that they have a good reason to forget all of MoP and be the Kirin Tor's dogs working for treats. Now they make the Blood Elves happy to be the Kirin Tor's sidekicks purely for the right to stand in the same room as humans. Before, at least they had the Kirin Tor needed them more than the Blood Elves needed the Kirin Tor going for them. Now it's literally just the Blood Elves preferring being second-class citizens who are hated rather than be respected magi of Quel'thalas where they'd be honored and their contributions to society valued.
The very least the Kirin Tor could do during WotLK is say "sorry for Ansirem and Modera doing nothing to help their fellow council-member Kael'thas, because they're more loyal to humans from a foreign nation than an elf who's served dutifully on the ruling council of their city for a very long time, prince of the kingdom that made all of this possible." And again in Legion, but Blizzard is saying that the Kirin Tor are in the right for unjustly purging a single ethnic group of their city for the actions of one, and Aethas and the Sunreavers and Horde are the ones who have to come crawling to beg them permission to be in their city again. And they have the nerve to make Ansirem (one of the two who completely abandoned Kael'thas and the most noble and powerful of his people he brought solely to help them) say "how do we know he won't just betray us again". Jaina, daughter of the admiral of Kul Tiras, who lived in Dalaran no more than 10 years if we're being generous saying that the Kirin Tor take apprentices who are very young children and thus haven't even mastered their reading and mathmatics, before she ran away to found Theramore, came back after like 10 years and called it "her" city, but doesn't consider it as being the city of people who've lived and worked with the humans there since before her grandfather was a glint in his old man's eye. She even says that some of the Blood Elves there are among those who taught humans magic in the first place. But yeah, it's totally her city more than theirs. She's like Harry Potter considering Hogwarts his home, only being very very aggressive about it.
"I believe that you will find that my gift to you is not just a profound duty—which it is—but also a delight—which it is! Magic must be regulated, managed, and controlled. But it must also be appreciated and valued and not hoarded. Such is the contradiction you must deal with. May you be dutiful ... and joyous both."
Malygos violated the hoarding in the process of regulating and controlling its use. Before the Nexus War, magic was completely unpoliced. There was nobody looking out to make sure it wasn't being abused. He had no choice. Magic was not appreciated by everyone. They took it for granted. The Kirin Tor hoard every magical artifact they get their hands on. The Reliquary USE magical artifacts they find, rather than letting them mold in a museum. Malygos did what he had to to do his Titan-given duty.
It's not stupid and shortsighted when it's the only option one has to accomplish their duty, because there's no way they can police the use of magic of so many people, millions/billions, while the Blues are so few, without forcibly taking it from everyone, at least temporarily, before returning it only to those trustworthy enough to use it responsibly.
K, Blizzard presents the story through modern morality, like making everyone appalled that they've actually won a crushing victory because winning a war while not having to write any condolence letters home to the grieving widows and children of your troops is totally evil, but w/e.
If they were presenting things with medieval morality, you wouldn't see anyone working with anyone. Every race would always see each other as savages, and would use their superior technology/magic to enslave them. They wouldn't see members of the other team as people. They'd see them as beasts, no better than cattle, and consider it their divine right and duty to "educate" them, and they'd do this by destroying their culture and using them for manual labor, prostitution, gladiatorial combat (to the death between two people, not Thrall's kiddy-hand gladiator matches in Durnholde, where he only killed animals Blackmoore pitted against him) for the amusement of the privileged few.
If it were medieval morality, Jaina would never have been leader of the Council of Six. After her father died, she'd be left destitute unless she could find a man who'd marry her, despite getting no dowry. Or she'd be some barmaid in Goldshire, fetching drinks and mopping floors. Or worse.
It's not weird that Alexstrasza considers her duty above that of her brother, but only when it's her brother killing mortals who refuse to accept his lawful right to fulfill his duty as given by Norgannon? Not when, say, Garrosh leads a slaughter through Ashenvale? Or Arthas purges Stratholme? She doesn't seem to care about preventing loss of life when it's the Horde and Alliance killing each other over petty issues like "oh, they're probably gonna get that ogre artifact and use it against us, so we have to go get it first and use it against them!" Or "man, we REALLY need farmland, so we should make a land grab for Andorhal. It's not like we have farmland any closer, only occupied by gnolls, murlocs, and bandits. *completely ignores Westfall* Nope, we need to destroy not one, but TWO massive deadly undead armies to get our farmland."
I'm not saying Malygos was doing what is right, because "right" is a subjective term. To him, it was the only thing he could do. To the mortal races, it was wrong of him, but only because they enjoy the comforts and conveniences offered by the Arcane.
If the Amani trolls were being decimated by the elves, or some other group that relies heavily on magic, and knew what was going on in the Nexus War business, they'd see Malygos' decision as "right."
Malygos was doing what he thought best for Azeroth, because evidence proved that the free use of magic by the mortal races resulted in chaos and devastation, every time.
Alexstrasza was doing what she thought was right when her duty is to protect life. The thing is, she apparently doesn't find her duty important enough to enforce all the time.
Eh. The only reason Alexstrasza sided with us is because we're the players and thus the protagonists of the story. If Malygos was killing all murlocs, gnolls, and kobolds because they were abusing magic, nobody would bat an eye.