You cn see her ghost at Anytime not just after her death. I whent in into church after the Shinra got to her and there was the "ghost"

Well actually... Sword thru the gut doesnt really prove her death... in the flashback in Nibelhiem... Cloud got stabbed in the gut and live... he even grabbed the blade and threw Sephiroth off the bridge...
Well if that didn't kill then she surly drowned when Cloud threw her in the water (Why?)