[quote=@Vocab]
If you were to, say, shut down the brain by directly manipulating the soul, then the person would stop breathing, their heart would stop, and they would likely die. 
[/quote]

Soul Gems are what contain the girl's consciousness. Magical Girls can survive even if their head is completely destroyed, as long as they're properly repaired with magic. 

I mean, they're basically liches. As long as their phylactery is intact and they're not witchified, they can't die.