Power users can disable it. For the less advanced users, impose that as default behavior as its pros and cons.
It happens because Firefox closes and re-opens libraries and permits an in-place update (and thus, breaking itself).
There must be some additional context here. I've never observed this behavior on Windows or on Linux (although on Linux I'm using an LTS release, which could be a confounding factor).
Obviously this is only a problem on Linux, because on other platforms Firefox's own autoupdater will only apply the update when Firefox is restarting.
In my experience, running software updates while using the system is a pretty bad idea in general. It works well most of the time, but there's a reason Linux* is the only system that allows that (every other OS defers applying updates to a reboot).
I do applaud firefox for supporting so much customization, as in this case. If I weren't able to disable this behavior I would have stopped using firefox immediately.