While there are definitely living Holocaust survivors today, most of them aren't up to doing half the shit Magneto does, and it seems to be affecting the impact his stories have on audiences. I remember reading Magneto stories as a kid in the 90s, knowing he was a little younger than my grandparents, and getting hit with a truckload of sympathy for the dude. He just wanted to have a normal life like Grandma and Granddad, and then the war happened and oh FUCK. Younger readers now are much less likely to have that personal connection; that's just how human lifespans work. And it's only going to get worse. Magneto does need some future-proofing.
That's not to say I think Magneto's origin should be changed, or that he should be permanently killed off. Far from it. This is comics; all kinds of timeline bullshit happens all the time. As someone pointed out above, Wolverine is most of the way into his second century of life.
What I'd do--and what I'm shocked Marvel writers don't seem to have done yet--is wave the mutant bullshit wand and make Magneto functionally immortal. Secondary mutation, maybe. Something something magnetic fields. The mechanics don't matter any more than "Wolverine is functionally immortal because healing factor" does. What matters is this:
At some point, Magneto will be the last living Holocaust survivor. And he will not let the world forget.
There was a story I read as a kid where Magneto took a handful of soil from the camp where his family died and spread it on the surface of the moon, where he was building a mutant haven of some kind. The image of him on his knees with soil running through his fingers and an agonized look on his face has haunted me ever since. To some part of him, it's always 1945. Never again is quite literally now.
I want to see Magneto as the furious conscience of the Marvel universe. I want him to rip a hole in the UN General Assembly building and stride in with his full regalia on--except for one sleeve, stripped to the forearm to show his tattooed number--and read the UN the riot act in all his nigh-unkillable glory. I want him to storm into summits between warring planets, atomize the ferrous metal in everyone's weapons, and lay down the galactic law that is There Will Be No More Genocides On My Watch, And My Watch Is Eternal. And I want future writers to use his story, and his enduring popularity as a character, to make sure that audiences don't forget either.
Magneto being a Holocaust survivor is only a flaw in the storytelling if you're a goddamn coward.