Is there a way of preventing me from being able to change the configuration of a part within a sub-assembly by clicking on the part in the graphics area? I am so used to changing configured parts in assemblies in this way that I find I make the mistake of changing the configuration of parts in sub-assemblies instead of changing the configuration of the sub-assembly.
I think that's part of the same "enhancement" we got a few years ago that allowed editing sub-assemblies from the main assembly without going into "Edit Component" mode (I still have trouble believing someone thought that was a good idea). Deleting parts from sub-assemblies when you intended to delete the sub-assembly from the main assembly was the more common problem with it, but I think your issue is probably related. It got a partial fix with SW2015: 2015 What's New in SOLIDWORKS - Deleting Subassemblies and Components of Subassemblies .
The best advice I can give is to try to get in the habit of changing configurations by clicking on the component or sub-assembly in the tree instead of the graphics area. Hopefully someone else will have a better idea.