This ignores that mutants policed themselves since the inception of Krakoa and the nation's morality only really improved over time. Literally one of their biggest, and only laws put human lives at the forefront. Any groups that threw their weight around and got into genuinely immoral activity were outliers and treated as such. The biggest exception being Beast, who got away with things and had his work largely go unnoticed, solely because some editors were afraid to stop Percy and just let him play in the corner, away from everyone else. But even then, the other characters called him out and he was basically one bad actor that they eventually had to put a stop to.
The diplomatic immunity was to help counteract how all the other countries and laws were rigged against them, and it still didn't just grant them carte blanche to crap over everything. We know that the X-Men weren't going to let mutants take too much advantage over this, and we even saw Cable and Cyclops handle Arakki who were haranguing humans at a bar.You know sorta like how the X-Men just decided that Mutants didn't have to follow anyone else's laws. Sorta how they kept criminals buried under their clubhouse in some weird limbo. Sorta how individual members just decided who gets to live and who gets to die, without trials or due process.
The Pit is an interesting example because it was meant for unrepentant mutants like Exile, who can't be let out anywhere else because they'd harm more innocents. (And let's be real, Sabretooth deserves the Pit. He literally can't be redeemed and would go out of his way to rape, pillage and kill the second he found himself anywhere else.) Yes, individuals decided who lives and who dies, just like how countries have judges and juries. People DID have trials, except for a few who Mags and Xavier Pitted in secret.
But most of all, the Pit was something that was meant to be examined and criticized. Xavier had good intentions with it, and in theory only the worst of the worst who refused every chance at doing good would be tossed in there. But the fact was that it could be inhumane, and that most of the prisoners had complex situations around their imprisonment that meant the Pit itself was an unjust punishment. Exposing the truth lead to people on the island protesting and fighting back against it... at least that was the plan, until the Krakoa era started dying and people IRL had to start start wrapping up their plans.
You know that keeping secrets isn't necessarily a bad thing, right? Nearly all heroes keep secrets, usually for the safety of those around them. Resurrection is probably the best example of this: once humans learned about it, Orchis lobbied for laws protecting those who kill mutants. Companies and countries tried to blackmail Krakoa into putting their heads in the queue. Probably unintentional, but Xavier, Magneto and Moira telling the Council the truth about Magneto directly lead to Terminator Moira and the Moira Engine/Sins of Sinister.The whole living on an island and keeping secrets speaks for itself.
Living on an island also isn't a bad thing. Unless you think those heathens in the Azores are secretly conspiring to rebuild the Portuguese empire and conquer the Western world. If you're talking about the society being isolationist, that it because it's a proven fact that the mutants need their own safe space, away from humans. And even then, portals allow mutants to connect with people all over the world and still have access to an escape. Select human family members were allowed on the island, and people could come and go as they please.
You should forget your definition for a sec. Not all superheroes fit that mold, even before Krakoa. Just because you have an idealized image of what a hero is in your mind, doesn't mean that all other images are wrong.It's not an outdated ideal. The idea that it is outdated is excuse to wipe away what is going on. A Hero by definition is "a person who is admired or idealized for courage, outstanding achievements, or noble qualities." . What exactly is noble about threating your friends of kidnapping their son? About killing your enemies when you really don't have to? About running and hiding in Space or on some orgy island? All questions are rhetorical here but the X-Men during this era have very little I would be willing to recommend of imitating.
The FF/X-Men mini should be ignored. I know it sounds like I'm moving the goalposts here, and I hate to be "URRM NO THIS DOESN'T COUNT BECAUSE I SAID SO." But it really is a special case. The mini was poorly-written and contradicted past continuity and lore to make everyone on both sides into caricatures and start drama, solely because they wanted to make this a mini. Because if this awful tome remembered that Franklin's family would totally be allowed on the island, that the X-Men were still at least cordial with the FF last time they met, and that Frankin could still live at home and just show up on Krakoa whenever it was cool with them (which was the outcome of the mini anyway,) none of this would have happened. It's like how AvX and IvX made no sense and required people to act like villains to make a story happen. At best, it's an exception that proves the rule.
I don't remember seeing the X-Men rounding humans into camps or trying to force them into changing species during the Krakoa era. I don't see them going around, kidnapping and dismembering humans. I didn't see them threatening to genocide all of humanity with poisoned medicine, then lead a disinformation campaign to frame their enemies for it. Your whole reasoning seems to be based around them killing people sometimes, without any respect for the context or how wildly, wildly different the situations and reasonings are.During the Krakoa era there is very little difference between the X-Men and the people that they were fighting. As an organization they have become what they oppose. Sure they have their reasons and I am not even saying that those reasons are ill intent. But how they operate and conduct themselves they are also the bad guys. The X-Men, during the Krakoa era, are no different that the Suicided Squad.
You can disapprove of them killing, but to say that keeping secrets, being jerks sometimes, and killing others in self defense/to protect innocent human and mutants lives, makes them as bad as Orchis?