Yes.
The entire point of Magneto, or at least the nuanced, layered version built on top of the mustache twirling villain of old is that he knows, absolutely with 100% certainty KNOWS, what will happen to mutants. Because he watched it happen to Jews. He lived it. It isn't theory, or fear, or paranoia. It WILL happen, in his mind, because it DID happen. He has seen evil destroy his people once, and now he sees it everywhere. Because how could he not?
Now, it doesn't have to the the Holocaust. Personally, I think it should be, for a variety of reasons. And I think there is enough wiggle room built into the mutant concept for Magneto to have an unusually long lifespan as a result of his mutation in addition to his powers. But it doesn't have to be. But yes, it has to be a genocide. An unequivocal, unmitigated evil perpetrated on people solely for something intrinsic and born of irrational hate. The character doesn't make any sense otherwise.
Now, that said, you could simply go with a much more standard villain approach. Then it doesn't really matter. Why do Bond villains do what they do? Because they're the bad guy! Nothing wrong with that approach, and it would mark their Magneto as different from the Fox version pretty clearly.
But, given some of the casting rumors appearing (and assuming, of course, that those rumors aren't all totally fabricated, which they easily could be), I find that unlikely to be the direction Marvel goes.