Нашел решение проблемы примерно так:

location ~ /bin/view/(System|System/.*|Main|Main/.*|Sandbox|Sandbox/.*) {
error_page 404 502 504 = @foswiki_auth;
}

location ~
/bin/(attach|edit|manage|rename|save|upload|mail|logon|rest|rdiff|.*auth).*
{
error_page 404 502 504 = @foswiki_auth;
}

location ~ /bin/.* {
if ($http_cookie ~* "adminid=yes"){
set $auth "_auth";
}
error_page 404 502 504 = @foswiki$auth;
}

location ~
(^/pub/Trash|^/lib|^/data|^/locale|^/templates|^/tools|^/work) { deny
all; }

location @foswiki_auth {
gzip off;
fastcgi_pass unix:/var/run/wiki/fcgi.sock;
fastcgi_split_path_info ^(/bin/\w+)(.*);
fastcgi_param SCRIPT_FILENAME
/opt/data/wiki$fastcgi_script_name;
fastcgi_param PATH_INFO $fastcgi_path_info;
fastcgi_param SCRIPT_NAME $fastcgi_script_name;
fastcgi_param AUTH_USER $remote_user;
fastcgi_param REMOTE_USER $remote_user;
include fastcgi_params;
auth_basic "Enter your WikiName. (First name and
last name, no space, no dots, capitalized, e.g. JohnSmith). Cancel to
register if you do not have one.";
auth_basic_user_file /opt/data/wiki/data/.htpasswd;
add_header Set-Cookie "adminid=yes;path=/";
}

location @foswiki {
gzip off;
fastcgi_pass unix:/var/run/wiki/fcgi.sock;
fastcgi_split_path_info ^(/bin/\w+)(.*);
fastcgi_param SCRIPT_FILENAME
/opt/data/wiki$fastcgi_script_name;
fastcgi_param PATH_INFO $fastcgi_path_info;
fastcgi_param SCRIPT_NAME $fastcgi_script_name;
fastcgi_param AUTH_USER $remote_user;
fastcgi_param REMOTE_USER $remote_user;
include fastcgi_params;
}

Лучшего варианта пока не придумывается. Может кто-то подскажет более
элегантный вариант?

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