If you find a way that works and got the time, give it a shoot.
My problem has to do with python reference which were still kept
alive, even if all the section of the model were gone.
in some other projects I managed this (reloading a Neuron model) but it indeed requires a painful process of eliminating all the python references made within the code.
neuronvisio.controls = reload(neuronvisio.controls)
I've used it here (https://gist.github.com/1211166)
However, if the GUI is running I think this doesn't really work.
Dunno if it helps!