I don’t think that there is a good way to do this. If you looked at the upgrade code in ACF you could probably create a cron that could do the work, but I think that it would take you as long to code this as it would to do the work manually for the sites. Luckily, DB upgrades for ACF happen rarely. The current upgrade is due to the change for using term meta. It could be that the reason it does not try to upgrade all sites at once could be because it can be a time consuming process, depending on the sites and if you have a lot of fields associated with terms. There is a possibility that it can time out. There have been reports of this happening on single site installations where there are a very large number of terms.
Sorry I can’t help you more.
Welcome to the Advanced Custom Fields community forum.
Browse through ideas, snippets of code, questions and answers between fellow ACF users
Helping others is a great way to earn karma, gain badges and help ACF development!