She wasn't evil evil. But neither was Juggernaut....yet people still complain about him going good.
I don't know that Magneto is completely evil on the level of Doom or Kang. Kang destroys worlds for the sport of conquest; because it amuses him, and because he can. Magneto is a traumatized jewish holocaust survivor, who's seen persecution of his people, and doesn't want to see another group he belongs to be persecuted; Mutants.
on the "Evil" scale, Kang, Doom and Loki would get 10s, Magneto would get about a 7 1/2, Juggernaut and Emma would (back when they were bad guy's) get about 3s or 4s.
A big part is I quit reading comics for 5 or so years in the 90s, and suddenly, not only was she good, she was an X-Man...