Is there a way to preserve my configuration between firmware updates? I had some apps installed on my Galaxy S2 and configured them on screen the way I liked to have them.

Today, the firmware got updated (it looks cool) and all my installed apps are gone from my workspaces. They are still available in the application menu. Also, a load of Samsung and Vodafone (my carrier) apps were put in the workspaces.

Is there a way to preserve my configurations between updates, and if not... why?

I usually use about five apps, so it's not such a big deal for me, but it's annoying. I can imagine some other users freaking out over this.
By workspace you mean homescreen ? 

You could try a custom launcher, like Apex or Nova, which allow you to backup your homescreens.