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Alright, like many comics, this gets kinda convoluted, lemme see if I can explain this:
I didn't read the issue where Wolverine "injures" him. That happened in Uncanny X-Men, I think, which I don't read. People assumed that Magneto died when Wolverine stabbed him up in there.
Anyhow, a very weird writer named Grant Morrison (The Invisibles, Animal Man, JLA) took over for New X-Men, which I do read. His first storyline was about Super-Sentinels destroying Genosha, and in New X-Men #115, they show a man in a wheelchair looking up as a Super Sentinel flew up and destroyed the building. Morrison later confirmed that Magneto, injured from Wolverine's earlier attack, was the dude in the wheelchair.
Does anyone stay dead in Marvel comics? Not really, but so far, he's assumed to be dead. One of the themes in New X-Men is how young mutants became disillusioned with the world after Magneto's "death", and started building giant statues and tributes to him. Magneto is being treated similarly to Che Guevara, where people wear his emblem and quote him and emulate him whenever possible. Basically, extending the idea that while his physical body is gone, his ideas are immortalizing him in people's minds. The other X-books are also acknowledging him as dead from the Genosha incident, so officially, Marvel is saying he died in New X-Men #115. Of course, some other writer could easily resurrect him for the hell of it.
Also, while Wolverine's "origin" was told in the Weapon X storyline, Marvel recently did a six-issue mini called "Origin", which is about Wolverine's childhood as Logan. So one can argue that Wolverine's origin was in Weapon X, and that "Origin" is merely "Logan's origin."
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