He feels bad about answering the call of nature because he has abandoned his obligations in civilization.
Gulliver has obligations to his job, his family, and society at large. This makes him have a lot of work to do and people who depend on him. He always fulfilled these obligations, but in heeding the call of nature, he left it all behind.
Gulliver is happy to be away from obligations, but at the same time, he is sad and feels guilty for abandoning them.
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