From the scene I assumed he intended to pierce her heart. The closest example I was remembering of is the renegade Doctor from The Authority, who was getting his head punched off by Apollo and was still able to reform and whup the guy. But even if Scarlet Witch's powers operated on a bigger scale, assuming she could replicate stuff from pastiches from a different universe, maybe operating under different rules, might still not sit well here.
And about her powers "only" operating on a planetary scale, wasn't there tie-ins and stuff during House of M showing her powers affected alien civilizations too?