Disabling CGI execution for a certain directory and every subdirectory below can be done by placing "ExecuteCGI = no" in a .hiawatha file.
Disabling access to a directory can be done via the UrlToolkit.
VirtualHost {
...
UseToolkit = restrict_access
}
UrlToolkit {
ToolkitID = restrict_access
Match /some/path DenyAccess
Match /another/dir DenyAccess
}