Corrected entry: Spock presents himself to Dr. McCoy in sickbay to be relieved of duty for "killing" Captain Kirk. However, as a medical officer, Bones has no place in the ship's chain of command. Doctors have an officer's rank in recognition of their education and value to the service, but no authority over military matters. (For example should Kirk, Spock and Scotty be indisposed, command of the ship would fall to Sulu who is in the chain of command even though McCoy has a higher rank) If Spock believes he should be relieved for breaking regulations and committing murder, and thus confined until court-martial, Scotty would be the one to do it, as he is the next senior officer. And this is not a character mistake, Spock quotes regulations regularly, there is no way he'd ignore chain of command. Contrary to what viewers seem to think, militaries have regulations and officers don't get to ignore them and do what they feel like! The only reason Spock talks to McCoy is so Kirk can walk out of the back of sickbay and create a nice emotional moment.
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Correction: McCoy is a full commander and is in the chain of command. There are several reasons Spock may have chosen McCoy, the most likely being that Scotty simply wasn't available at the time. In any case, you're assuming regulations in the future must be identical to regulations in today's military. In the future, the regulation may simply require him to turn himself into the the first available officer above a particular rank. Spock also knew the reason for his killing of the captain was directly related to his mental state, which would fall under McCoy's expertise.