Ok im thinking on this but what ive come up with so far is probably incorrect.

"Covered with sackcloth vile they seemed to me" People who usually are in sackcloth are traditionally either poor, repenting for something or are humbling themselves.

"Appeared to me with laden and living boughs
Another apple-tree..." sounds like an allusion to the forbidden tree from the garden of Eden. So this passage is probably talking about forbidden fruit.

Ok "thither" can mean to a place, point, end, result, being on the farther side from the person speaking, or can be applied to time: n the thither side of, older than; of more years than. So the phrase "From having but just then turned thitherward" can be about turning away from someone, looking to the past, or the narrator has just gotten a new goal.

"Saw people mudbesprent in that lagoon". Ok mudbesprent. Mud is well mud. Besprent means sprinkled over or stewed. So mud stew, yummy. I guess that mudbesprent could also be a creative term for burial. So people buried in a lagoon .

Ok the definition of a castigator is one who castigates or corrects. So castigate=correct. But that doesnt make sense with the rest of the phrase. I think that in the context of "People, whom the black air so castigates?" castigates means corrects. So People whom the black air so corrects ?

Your clue is not helping me much and this is all i can think of at the moment.