In order to exclude a specific path from a rewrite directive, put the rewrite inside of a location block and create another location block for the specific path. E.g:

server {
    listen 80 default;
    server_name example.com;
    root /var/www/html/;

    location ~ \.php$ {
        try_files $uri =404;
        fastcgi_split_path_info ^(.+\.php)(/.+)$;
        fastcgi_pass unix:/var/run/php5-fpm.sock;
        fastcgi_index index.php;
        include fastcgi_params;
    }

    location / {
        # An example rewrite
        rewrite ^/(.*)$ /index.php?param=$1 last;
    }

    location /pro-sites/ {
        # Do nothing. 
    }
}