You can't defend too many of Spock's actions in this episode unless you resort to making excuses for the inconsistancies.
Lol, welcome to star trek. Making excuses for inconsistencies is the name of the game.
And, like I said, while it's obviously an oversight by the writers, it's really not
a leap to think that stun may just not have been effective. We've seen it Trek since then.
An even more absurd aspect of this episode, that hasn't really been addressed in this thread, is the idea that this is Spock's first time in command of a mission. Really? A first officer of one of the federation's best ships that's never even been in command of a routine shuttle mission?
Take the episode for what it is, it's a first season episode, the 14th episode of trek ever produced, and like many first season episodes(of all the star trek series), there are inconsistencies and errors. TOS had the best first season of any Trek, but they were still figuring things out.