Ben Finney was Kirk's greatest foe.
It took Samuel Cogley to get Kirk's ass out of the fire that time, and also it was an extremely stressful situation all round for poor Kirk.
Kirk can cope with ship battles, fistfights, and any command situation. He can have foe's who are a challenge but he is premiere league himself, he doesn't have his heart ripped out.
But to really hurt Kirk, take his power over a situation, accuse him of things he never really did but without any ability to show he is innocent. That will destroy most people and Kirk nearly went down for Finney's murder. Although to be honest how on Earth Finney planned to leave the Enterprise and remain hidden long enough for Kirk to face any kind of prison sentence is beyond me.
You make an interesting point. Ben Finney in his way was a good enemy. His strategy to humiliate and frame Kirk was effective and was effective again in Star Trek 6