Might it be possible to have a list of commands generated to have the command-line tools re-create the same change? This would be ideal to automate configuration changes for clusters or groups of similar workstations: configure a service like samba on one of them through the gui and have a script to make the same changes on all the other machines. In my optinion this will be more powerful than a centralized configuration solution since the same script can also be applied to new installations (e.g.a post-install script for a kickstart installation).
We're planning to have the middle layer log changes in some way(including what files were changed) and there are a lot of good reasons to make optional components available which do other things with config changes (modification detection, copying to multiple boxes, creating a script to get from state A to state B, etc.). To do things like managing users, changing hard drive settings, etc. it may turn out that this type of change to set of commands translation is necessary.
A frontend that can replay the logs from the midlelayer might also be a good solution.