What that code does is stupid, yes. It shouldn't remove the original unless the platform is win32. *Windows* (except with Transactional NTFS) doesn't support an atomic rename, so it's no surprise that Python under Windows doesn't either.
You're seeing a zero-length file because Tso's fix for ext4 only applies to files being renamed on top of other files. The filesystem should be fixed to allocate blocks on *every* commit, not just ones overwriting existing files.
As for the program -- fsync should *not* be inserted. (Though the unconditional os.remove() should be changed.) It's a bad thing to ritually fsync every file before the rename for a host of reasons described upthread. Just fix the filesystem.