Jean didn't mind control Kitty's parents.
The second "Jean" declared herself Phoenix, that was the Phoenix force posing as Jean. Jean was basically a non-entity her first time around as Phoenix. When the Phoenix was first revealed to be a separate entity, they even went as far as to say that that wasn't even Jean's body but a duplicate though this has since been ignored by several stories.
That wasn't the original intent behind Phoenix, but it's been the canon for decades.
Edit: As For Magneto, the one and only time Magneto actually attempted Genocide it was quickly revealed to be an imposter. At the absolute worst he's willing to kill humans to prevent mutant genocide if he has to. He hasn't consistently been a villain since the 80s.
And when did the X-Men torture innocent scientists to death? Not in this arc.
Mystique's incarnation fo the Brotherhood of Evil Mutants burned Moira to death in an alternate timeline, but that Mystique wasn't an x-person and that didn't happen in this timeline.