The God-Emperor was a man who became a god, the chaos gods are older than him except for slaanesh. He is doing what he can, and we too must do our part.
Yes, the emperor rots, but he rots to stop the merging of realms.
Depends on what you define as 'protecting'. Does being the Light of Holy Terra, which is in fact, giving the human race an FTL method to protect themselves is a form of protection? Or does he has to fight in the frontline, purging xenos or the like in his flesh-and-blood? To me, there are ways for a leader to protect their subjects.