And I suppose Link stabbing Ganon in the head in OoT didn't happen?
In OoT, Ganon's established weak point is the tail and every other part of his body is invulnerable. In gameplay. Cutscenes, on the other hand, say that Ganon is vulnerable to the Master Sword everywhere, such as when Link attacks his face.
The Ganon in ALttP had the full Triforce and was fighting in the Dark World, where his power was absolute. A strike from the Master Sword to any area could harm or paralyze him. The Silver Arrows kill him. In gameplay, but there are no cutscenes to speak of.
In TP, Ganondorf transforms into Ganon, and can be attacked on his stomach. Of course, that was the scar where the Sage's Sword struck him. It also hit his heart, like Zeus, and didn't kill him.
Anyway, Zelda is still firing Light Arrows at Kratos, which very well could incapacitate him.