The only way to "free the command line" in MATLAB is to run your code with a timer, or in response to a callback (such as as a serial port bytes available function). The function that is run must return fairly soon, as the command line would not process commands while the function is running.
pmode does not free the command line. None of the facilities in the Parallel Computing Toolbox free the command line.
In some situations what is needed is not that the command line be freed, but instead that the user be able to trigger interactions while the code is running. In such cases it may be possible to build a GUI that has buttons or controls that allow parameters to be configured and then to trigger an action, with the action being executed in the context of a callback for the graphics object. For this to work, the main looping code that is executing must cooperate, by periodically permitting any pending callbacks to be executed, by calling pause() or drawnow() or waitfor() or uiwait()