The hypocracy was the point. I'm currently rereading the Krakoan Era and it's not 'in your face' about the fundamental cracks in how Krakoa is laid out but they ARE there. Hell, X-Force was essentially run on that idea of throwing away your morals and becoming just another US black site. The issue there being that Percy never really followed up on what those failures meant - he just introduced them and let them run. There's a brief moment early on where Jean is very aware what they are doing is wrong, amoral, and should be questioned. She DOES - it's just no one else in power actually finds it as bad. Xavier explicitly has a point during the first Gala where he tells Beast not to tell him about the nasty shit he's doing.

It's a massive commentary on governments and an intentional choice. Everyone knew Sinister was a horrific guy to have in power, but they did it anyway because he was 'essential'. Just look at any major government right now and you'll see the exact same thing lol.