One trick is to workaround this git limitation is to add an empty .gitignore in the empty directory. This doesn't affect svn and the directory is no more empty from git's point of view. Here is the bash one-liner to create this .gitignore, to be run from the project root directory.
find . \( -type d -empty \) -and \( -not -regex ./\.git.* \) -exec touch {}/.gitignore \;

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