The situation with Emma was a last ditch attempt to try and make the Inhumans seem more reasonable in the conflict by having one of the X-Men go full on genocidal against them, and even that didn't work; people still love Emma and very few cared for the cannon fodder she offed.
I think that was the central problem with the conflict. The X-Men being reactionary and wanting to destroy the Terrigen cloud was somehow meant to be taken as just as morally ambiguous as the Royals just sitting back and letting mutants get gassed to death because "Yeah, but our powers...
," and somehow the writers were still surprised that the Inhumans came off looking like the bad guys in the drama.