Yes, I was also about to suggest mod_rewrite. Should be possible to match on your secret hidden filename and return content from a “shadow” directory structure that only contains those files.
You could generate those files in the shadow structure on the post-commit event. I have rewrites within the mod_dav_svn location in order to provide additional REST functionality on svn paths. Merkle-tree sounds interesting, let us know about your progress. /Thomas Å.