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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. Apparently these sailors had never read the Romantic Poets. Nature, in all its glory, should not be disrespected. They did not understand that, "all creatures great and small the lord God created them all." You are right, the sailor was not crazy or mean spirited. He represents the folly of man, his arrogance and his meekness in the face of nature's awesomeness. Fortunately there is a lesson in Nature's karmic body slam, the Mariner blesses the snake and finds a little redemption.