I agree that Destiny is weary of a radicalised and zealous Moira manipulating Xavier and Magneto but from all the little hints we can also glean that perhaps from 10 lives Destiny saw 9 defeats for mutantdom and one victory alas that victory may be pyrrhic because to get there Xavier and Magnus have gone increasingly jingoistic and have imbued mutandom with identity and culture but a warrior and honour culture(through crucible or embracing Arrako as examples) and embraced social Darwinism(Sinister is nobility on Krakoa and Xavier's mission to the vault probably has less to do with threat analysis than technological espionage imo). Now maybe Destiny's animus is from knowing that Mystique will be manipulated or the fact that she herself won't live in this 'eden' or it may just be that this one win may hasten mutantdom's destruction from alien forces that will perceive earth as a higher form of civilization much sooner perhaps because of Xavier and Magnus reaching for the stars with S.W.O.R.D. There are questions of doubt planted through the saga, Nightcrawler questioning crucible, Legion smelling secrets and a sinister force(Onslaught) and all the manipulation.So Destiny may be seeing a dystopian future because of Krakoa, that may be unpalatable to her, not only because Moira just cannot see it, but that mutantdom at its peak will lead to its greatest destruction because of a very human trait-hubris.