What does this mean? “Through its grandiose certainty, its sheer assertiveness, it manages to satisfy the clergy while at the same time expressing the problem with faith: that faith, any kind of faith, and regardless of how adamant it might appear, is a space of doubt.”

I think it means that that no matter how strong your Faith is there is always room for doubt. When the Black Death came even those who were faithful died. This lead others who were had a strong feeling for their faith to question their faith.

I think you're right.

Here are a couple of corrections for your write-up:

This led others who had a strong feeling for their faith to question their faith.