Your users could configure their web servers to have mutliple directories that act as cgi directories. With Apache you simply add the lines

#
# ScriptAlias: This controls which directories contain server scripts.
# ScriptAliases are essentially the same as Aliases, except that
# documents in the realname directory are treated as applications and
# run by the server when requested rather than as documents sent to th
+e client.
# The same rules about trailing "/" apply to ScriptAlias directives as
+ to
# Alias.
#
ScriptAlias /cgi-bin/ "/var/www/cgi-bin/"
ScriptAlias /alt_dir/ "/var/www/alt_dir/"
[download]