There's more than a few ways to kill Wolverine.
^ Starting with that. Wolverine can heal from almost any injury, given time... But if he were blasted by a huge Sentinel beam and flayed down to just a skeleton (like he was here), he wouldn't be able to recover.
He could also be killed by removing his head from his body, though with the adamantium spine keeping it firmly in place, that'd be pretty hard to do.
Magneto, having complete control over Wolverine, could fly him up into outer space, or hold him under water until he died of suffocation.
There are other, more obvious methods, like canceling out his healing factor, but nobody really takes those into account, 'cause they're boring.