Do you have shell access? Can you change permissions on directories? If you remove the read bit for the user that the webserver will be accessing your files with from the directories then the web server will not be able to get file listings, however, any URLs can be served up normally.

Ususally this should be enough:

chmod o-r <directory>
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If the http user is in the group that owns your directories, then you may need to do this:

chmod g-r <directory>
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However, that could put a hamper on collaboration efforts if many people update the site using a common group. And never remove your own read permissions to the directory. You won't be able to ls the directories yourself. But you can easily put it back. You can run this on your whole web tree in one command:

find . -type d -exec chmod o-r {} \;
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Cheers