They beam down ten and a half miles from the nearest village (feeders of Vaal), Hendorff isn't killed until they take their first steps toward the village, at that point the transporters still work (the body is beamed up).
Then the Enterprise start to lose potency in the antimatter pods, but they can still transport up and the ship can still leave.
The real trouble starts after the incident with Spock and the exploding rock, in case you didn't notice, when the planet's natives are feeding Vall, they're feeding it these rocks. Spock is messing with Vaal's food. Only then does Vall shut down the antimatter pods, shoot at Kirk, shut down the transporter, and kills Kaplan with lightning.
Debateably, Scotty could have left orbit at this point. Only later came the tractor beams.
Supposition on my part. At one time the People of Vaal were a technologically advanced species who decided to make a change to a simpler lifestyle, but they didn't want to be completely primitive. So they hung on to a lot of their technology, they just made it automatic. They had weather control, planetary defenses, agricultural control, their medical science had given them long life and perfect health. Over time the original members of this species died and there were replacements or descendants. And they lived a life of peaceful existence until the day that the Federation came and destroyed it all. The Federation didn't believe in their rights, their diversity or their choices.
That's supposition. What isn't supposition is the fact that Vaal didn't build itself, the people of that world created it for their own reasons. In destroying Vaal the Federation (through Kirk) created a entire planet of people, perhaps many millions spread all over that world, who now were actual primitives, and defenseless.
Spock delivers these points to McCoy:
1) Doctor, you insist on applying human standards to non-human cultures ...
2) Another is their right to choose a system which seems to work for them ...
3) Doctor, these people are healthy and they are happy ...
4) What ever you choose to call it, this system works
The second, third and fourth points might be tenets of the PD. The second certainly should be. The people of Vaal were too weak to say no, don't destroy our culture. Part of the Prime Directive that is directly quoted in Bread and Circuses is; "No interference with the social development of said planet." The Federation hardly respected their particular choice on social development.
McCoy: Learn sex from a machine? Now that's something I'd like to see.