I hope the human-apologism is exclusive to Logan
By minority you mean "the entire functioning government of every single nation on the planet".
Plus every member of groups like the Friends of Humanity (estimated members 250,000), the Purifiers (estimated members: 500,000), and the other anti-mutant organizations (including SHIELD, SWORD, AIM, etc)
Legion/Nate Grey/Jamie Braddock/Mikhail Rasputin rewrites reality long before any of that. Storm can control individual molecules of everything in the air (if her fans on here are to be believed), so she kills every human from Krakoa.
Face it, in a war, the Avengers lose badly. Their entire full power force was nearly beaten on Utopia by ten mutants, most of which weren't trying.
Everyone seems to have conveniently forgotten about all the bad stuff evil mutants have done, such as Magneto going full on Hitler during Grant Morrison’s run. And let’s not even start on Sinister and Apocalypse. But, sure, Logan is a traitor for not blindly wanting to kill all “flatscans.” Welcome to 2019 I guess.
Depowering serum at the cost of immediate execution if they elect not to allow themselves to be injected. No different than saying "you're gay? Well, here's a pill that will make you not gay. Or we can put a bullet in your brain. But it's totally your call".
And if one of two choices is immediate execution, it's still very illegal and very wrong.
First Where are those numbers? in the marvel wiki I dont see that estimations, where is stated that these organizations are so powerful? Because they always seemed to me like a gang of losers with less than 100 members that need to make deals with real bad guys like HYDRA to have some relevance ( and purifiers have mutant leader , never forget that)
Funny that you mention Sword and AIM because both organizations have been directed by mutants at some points. And currently SWORD is directed by a mutant again. And SHIELD didnt exist since two years.