It's still not clear to me whether creating a directory with permission of 751, had any effect at all, or whether there is anything at all you can do to make things a little more difficult to access.
On most filesystems directories can be thought of as special files that hold a list of file records. With a permission mode of --x (no read, no write, execute), a user can access files within a directory but not the directory itself (the directory contents, or list of files in a directory, will be inaccessible). For instance,
opendir("/home/fguy64/public_html/forbidden") would fail, while
fopen("/home/fguy64/public_html/forbidden/foo.class", "r") would succeed. To put it another way, the execute bit allows anything to pass through a directory when a path is traversed. If you don't have
directory indexing enabled for a given directory, removing the read permission won't be beneficial as there is no way for a visitor to read directory contents. It may have unintended effects on your site internals, but those effects aren't what you're looking for.
You can't prevent downloading, but you may be able to use the
java.AppletAPI to check non-forgeable (well, difficult to forge) information about the document in which the applet is embedded.
getDocumentBase would probably work. Note that this implementation will have its drawbacks (should you change the host URI in any way, you'll need to recompile) and won't be 100% effective (a downloaded applet could be patched in place or decompiled).