I wonder if Chain of Command might not be too cerebral for TOS. Seeing Kirk being tortured as brutally as Picard was, might make a more naive 1960's audience a bit squeamish. They might also wonder "why doesn't he just escape"?
This is all sort of an odd exercise anyway. Retrofitting an episode from a 80s-90s ensemble series of 9 players into a 60s show with 2-3 leads and lower billed supporting cast means major story revisions. Network censors and broadcast standards have to be considered in the context of the 1960s-- easily done, if you lived during it. The severity of Kirk torture scenes couldn't be as explicit as in Picard's. TOS did dabble with it a bit, using agony booths, neural neutralizers, agonizers, and various alien torture devices and experiments. "The Empath" was pretty brutal compared to what was being seen on other shows then.