I don't think Thor will be crushed by Magneto. He was shown to be extremely durable through his movie and the Avengers.
The only things that have shown to cause him any kind of damage is Hulk's punch which is strong enough to stop a giant flying armored monster, and Loki's Asgardian Knife.
Never mind he took a Frost Giant hand to the head which can break Asgardian Metal. He took Odin's staff blast to the chest.
He also survived that ridiculously high fall, or insane crash which ever way you want to look at it.
All without injury.
We also know Asgardian Metal is bullet proof.
But even if Magneto can restrain Thor in his armor. Thor can still summon his Tornados and Lightning to the area without having to move. He summoned that massive tornado against the destroyer without having to whirl his hammer about.