You could do it with the API by looping through the websites (with Recursion::Infinite) and updating the crontab on each.
Recursion::Infinite
I think us having the default set to WordPress Cron disabeld is a big mistake. I personally find that SO MANY THEME's having issues importing their demos because of this.
slimx a big mistake
I disagree. wp-cli cron is the best way to do things.
slimx we found increasing max execution time helped with this. its also why we are keen to set the cron time to something like 15 minuets globally.