It seems highly unlikely.
The second part of the Guns, Germs and steel, featuring Efrain Trelles, that you mentioned in the question is currently available to view on YouTube. A transcript is also available online. From the transcript:
Efrain Trelles: "Ataxalpa knew that the Spaniards were not gods. The intelligence reports speak of people wearing wool on their faces, like a lamb or like an alpaca, they’re just like an animal. Then they went from one place to the other wearing on top of their heads a little pot that has never been used for cooking. You need to be crazy to walk with a pot, but you must be beyond salvation if you arrive to a camp and you don’t use that pot to cook."
There is no mention at all of Inca priests eating human heads.
This is not one of my specialist areas, but there are a lot of texts available on archive.org. I haven't been able to find any mention of either claim being made in contemporary accounts of the Inca.
In fact, the Inca did not use metal cooking pots. In her 1994 book, America's first cuisines, Sophie Coe references the account of the Spanish Jesuit priest, Bernabé Cobo, who said the Inca cooked by placing heated rocks into a large earthenware cooking pots [Coe, 1994, p175]. They also used Paila, or shallow earthenware bowls to cook in ovens.
It seems unlikely that the Inca would confuse a steel helmet with a ceramic cooking pot, particularly since the Spanish also wore steel breastplates. Furthermore, as @OON has pointed out in the comments, the Inca also wore helmets. This feels more like a modern elaboration to the story of the conquest.