If the update included a major update to the launcher (the app that provides the desktops and app drawer) it might make sense, but that's not going to be every update. And when you say "android update" do you mean the very occasional android OS updates or the more common security patches as well? I really can't imagine why the latter would do this. So I'm a little surprised by this. Mind you I never use the stock launcher anyway, so I'd probably not notice what updates do to that.
So that's one work-around: use a third party replacement launcher (like Nova, or one of the many others) rather than Samsung's launcher. Then your desktops are nothing to do with Samsung's software, and an update certainly won't change them.
I don't suppose Samsung provide a way of backing up your desktop setup? That's the only other thing I can think of.
No, root won't help you there. Indeed applying OTA updates to a rooted phone is a bit of a dodgy business in itself, and many manufacturers' systems won't update modified phones anyway. So if you were to root (which you don't want to) you might have to apply your updates manually.
