Wonder how this fits into the story
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I think we have to consider exactly what despair means in the Christian context. I find this definition from the New York Times pretty good,
"Despair is by tradition the sole sin that cannot be forgiven; it is the conviction that one is damned absolutely, thus a repudiation of the Christian Saviour and a challenge to God's infinite capacity for forgiveness."
So, despair separates the person from the eternal saviour (yes that would be God). Faustus "repudiates" the saviour for much of the story. The good angel really tries hard to stop Faustus from making a sinful buffoon of himself but to no avail. Faust does not even really believe in God despite this angel sitting on his shoulder. This is essentially what despair is, the absence of belief in God's salvation even if he sends an emissary to camp out on the person's shoulder. Faust prefers wallow in his sin even when the angel offers a full pardon. Instead Faust relies on other "supports" like Mephistopheles (wasn't he a great friend!) or Helen. Faust's constant rejection of God's salvation, until the end, is thus considered despair and one of the more serious sins during Marlow's time.