I have this exact same problem. I can organize the TOC to remove the assembly node at the top and just list namespaces but then I get duplicates -- one namespace entry each time that namespace appears in a different assembly.
Assemblies are not a big concept in our product and I need a way to either collapse the mutiple namespace entries in the TOC or modify the TOC names to include the assembly, eg
Namespace_Name (Assembly_Name)
I can't figure out how to do either thing.