It can be done, but it's a little tricky because you can't have <Directory> sections in htaccess, so you need to put a separate little htaccess file in each directory that you want to protect.
It's a single line: Header set X-Robots-Tag "noindex" If you wanted to, you could add a <FilesMatch> constraining it to specific filenames or extensions-- but I don't suppose your page files are surrounded by non-page files in the same directories that you do want indexed.
But wait! This can only be done if you're dealing with real, physical directories. You said joomla. Do those / slashes in the URL represent physical directories?
:: wandering off to see if there's a way to set headers within mod_rewrite ::