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On the surface of things the Mariner kills the albatross because he figured the lack of wind was all the bird's fault. The men were petty creatures. When the wind blew it was all "good albatross" but when the wind stopped it was all "damn albatross". It is human nature to blame something when things don't go our way.
When the great bird is killed, the men cheer. Nature, however, has some serious payback coming at them.