I think that you are supposed to see then in a grey light. The X-Men hadn't been acting like villains, even if the language seems to be more agressive (understandable considering the circumstances), but there is definetly something off about Krakoa and letting all the villains in, no matter how yoy sliced it, is an incredibly questionable idea at best. I also find strange how everyone seems to be ok with the idea and no one had shown much doubt about Charle's vision (especially considering that Xavier has been less than trustworthy in recent years), except for Wolverine. But that might have to do with the poor transition between status quo.