Chain of Command could easily be done as two separate unrelated episodes. Part 1 would become a single episode of an action-packed spy mission. Lots of fun physical stunts for Shatner-Kirk. In this pre-imagining, Kirk does a successful escape, beaming out just in time. Jellico would still be the main guest star, butting heads with the enemy [random race] and Spock, to McCoy's dismay.
Former part 2 could open with Kirk already captured by a different [random race], physically and psychologically tortured by bad guy Madred, while Spock and McCoy try to rescue him. And Shatner gets to give us extra ham, hold the shirt.
And since we're fantasizing, my guest star choice works for either Jellico or Madred. I think it's a shame Leslie Nielsen never guested in 60s Trek. He would have been a natural for one of Kirk's old friends gone bad. He was popping up a lot in those days, often as evil authority figures. He had science fiction experience. Those who only know him from Airplane and Naked Gun would be surprised.
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"?