Umm, why do you people think Spock had done no command jobs before this shuttle sortie? Nothing of the sort is actually said in the episode.
All we have is a remark from McCoy: "It's your big chance". Spock is beduffled as to what McCoy might mean, so the Doctor explains that Spock always wanted to lead by logic: "You've never voiced it, but you've always thought that logic was the best basis on which to build command. Am I right?"
So all we learn here is that, as far as McCoy knows, Spock has never before been able to conduct a leadership task by using pure logic as the basis. Which means he could have performed lots of leadership tasks, only he had to follow illogical human customs and take into consideration illogical human sensibilities in those tasks. Now he is isolated from the rest of Starfleet, and can finally do things his own way. Which, as we learn, ain't exactly the best possible one.
McCoy never claims Spock didn't have prior command experience, and Spock never alludes to this, either. None of the bit players dare suggest that Spock would be a greenhorn, either. So there really isn't any dilemma on Spock's putative lack of command precedent, not if we go only by the material given in the episode.
Timo Saloniemi
Actually toward the end of the Episode while the shuttle was in the decaying orbit, McCoy says something to the effect of "so ends your first command."
And Spock not only doesn't contradict this, he outright agrees with McCoy:
McCoy: Well, Mr. Spock, so ends your first command.
Spock: ...Yes. My first command.
That's pretty unequivocal.