Being okay with Krakoa does not make a character morally grey. Emma is morally grey bc of what she did to Shaw, hiding it from the Council, not to mention condoning the questionable things the Maraurders have done such as maiming people. I dont think Scott or Jean would be okay with any of that and would call her out had they been present
And FYI, Scott was already back to being like this before he and Jean reunited. We saw that in the 15 issues of Uncanny that Rosenberg wrote. He and Emma werent aligned in their ideologies there either. He was brought back with a back to basics persona and that had nothing to do with sticking him back with Jean. That came later