Actually, the X-Men in the Krakoa era operated more like the Mafia than you think. In fact there are direct comparisons. The origins of the Mafia consist of group of Sicilians who formed groups to protect themselves from persecutions and hostility. They then formed their own system of Justice and Retribution and often carried out both in secret. Eventually, this same group would use their power to take advantage of others and commit crimes.
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 whole living on an island and keeping secrets speaks for itself.
It's not an outdated ideal. The idea that it is outdated is excuse to wipe away what is going on.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.
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.
As to not being cruel or malicious... did you read the books?
These are your "heroes" now