From what I understand, Harrison was just going to be a Jason Bourne type character on the run. Admiral Marcus, being the real big bad, bombs London and paints Harrison as the terrorist that needs to be killed on site because of all the secrets he has of Section 31's dirty work. Harrison tried escaping Section 31 because he thought Marcus was going too far with the preemptive strike against Klingons. This is why you have that whole sequence of Kirk and Khan working together to stop Marcus, because Harrison was just supposed to be a good guy. Somewhere down the line, Lindelof convinced the writers in making Harrison into Khan, which shifted the dynamic dramatically during the rewrites.