Running WP Cron on multisite the right way

I think the best way is to use WP-CLI but you’d need to write a bash script to do this. Here is one that should do it for you:

WP_PATH="/path/to/wp"
for SITE_URL in = $(wp site list --fields=domain,path,archived,deleted --format=csv --path="$WP_PATH" | grep ",0,0$" | awk -F ',' '{print $1 $2}')
do
    for EVENT_HOOK in $(wp cron event list --format=csv --fields=hook,next_run_relative --url="$SITE_URL" --path="$WP_PATH" | grep \"now\"$ | awk -F ',' '{print $1}')
    do
        wp cron event run "$EVENT_HOOK" --url="$SITE_URL" --path="$WP_PATH"
    done
done

You’d then need to add this script to crontab and run it maybe every minute if you like