This might be more likely related with backend (yum in my case) however since packagekit can fix this, it is related as well.
While doing system update, after downloading packages, applying updates slows down the overal system. That causes unknown locking of UI responses and such. From user point of view that is random thing to happen since s/he wouldn't know if there's an extensive background operation happening. S/he would blame OS in general for this kind of things.
I have no idea what's the real cause of this slowdown but maybe it's because update process is run with high priority (nice value) even though it's importance is much more less for user at the moment.
If there is nothing to prevent this slowdown, a notification when the Update begins with a message saying 'Your system is being updated, you might experience occasional slow downs during the update.', even better with 'do not show me this' checkbox. Finished notification might be useful as well. We can limit notification constraint to big updates since slowdown is more noticable if big packages are updated.
Windows Update is doing this kind of thing as far as I remember, saying also don't shutdown or unplug the computer. We might need that as well.
This is a bug from the Linux Kernel... desktop applications can't really deal with this (and even so, if that was the case, it would rather be yum's responsibility as I understand it).