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a locked up GUI is only likely to become a problem once you have an infinite loop, i.e. because you forget to put a HLT statement into your code, otherwise all code is likely to be executed immediatley until it finishes, so that the GUI will be responsive again directly after having finished the simulation of the program.
So, threading, be it the GUI or the simulation engine, would only really help to debug a non-trivial program while it is *running*, assuming it would have to run longer than just a couple of msecs or seconds.
Note that even running the program in debugger/step by step mode, will NOT lock up the simulator because the engine will return control to the UI, once a statement has been executed.