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I agree that making the code match the docs would be preferable – an unexpected KeyError might be easier to track down that way but it'd still surprise most developers.
re:pwd docs, the formatting in https://hg.python.org/cpython/file/8e9df3414185/Doc/library/pwd.rst makes it easy to miss the KeyError note – it's at the end of a paragraph after a table and since "entry" is a generic term it's possible to misread it as applying to fields within the record rather than the record itself. I think it would at least be worth adding a newline and perhaps explicitly noting that it applies to any function which returns a password database entry. 
Given that there are only two functions which it applies to, it might be best to simply add a note to each of them for people who use "pydoc pwd.getpwduid" or an IDE and don't see the module-level docs but that's getting a bit contrived.