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Believe it our not, dealing with the absence of those system calls is more contained than you'd think. What is pretty nice about Python is that (almost) all of the file system operations are performed through posixmodule.c. Most of the changes in that area are thus made to that source file (and configure.ac).
Furthermore, it looks like posixmodule.c can be simplified a lot. What makes it so incredibly complex right now is that it wants to fall back to non-at() operations in case no directory file descriptor is provided, which is not needed. If that would get fixed, we'd kill two birds with one stone: the code would get a lot simpler, while almost automatically gaining support for CloudABI. But let's save this discussion for a separate thread.