Comment # 8 on bug 1178799 from Danilo Spinella

I see, if it works like this, it makes sense that is breaks. Unfortunately,
since the mariadb instance is managed by akonadi and not by systemd as a system
service, I can't think of anything that can be done to prevent this, as it
currently stands.

Is this the default configuration of akonadi? Or is it your custom
configuration? I'd instead use a single system instance of mariadb, handled by
systemd. In this case, the mariadb package stops the server before updating it
and then restart it, so there shouldn't be any breakage.