New here, but couldn't resist chiming in.
I think Saavik is a good candidate for IC because she contradicts Kirk by quoting regulations throughout the story. When Kirk ignores her advice, that decision causes a major obstacle by allowing Khan to severely damage the ship.
Having said that, I think you could make an argument for Saavik being the MC and Kirk being the Protag. It seems quite a lot of the story unfolds to Saavik as it does us, including the plot "twist" where Kirk's plan to deceive Khan works. Just a thought.