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.
We don't really know who built Vaal. For all we know, it could've been the Preservers.
I doubt Scott had the authority to break orbit without Kirk's orders.
The issue of whether the Enterprise crew brought Vaal's wrath upon themselves is an interesting angle. But when Kirk began fretting about his "orders" and how he should disregard them, it was Spock who reminded his captain of their mission to be there.
The Prime Directive wasn't brought up until much later in the hut. And you'll recall that Spock had misgivings that Starfleet Command would agree with Kirk's plans. This seemed to me to be a clear indication that the Federation did leave loopholes in that directive.
The Sigma Iotia incident ("A Piece of the Action") has also been brought up in this thread. Was Kirk wrong? Was the Federation wrong? I'd say in the "present tense" (TOS era), the answer was "no" to both questions. The episode strongly indicates two things: (1: the Starship Horizon's first contact with Sigma Iotia predated the Prime Directive being codified; and, possibly... (2: the Horizon could have herself been pre-Federation. IIRC, the Horizon was never referred to as a Federation starship. It could be that the Enterprise was dispatched to the planet only to take responsibility ("in for a penny, in for pound") for the Horizon's prior interference regardless of who actually sowed the seed.
A similar issue would be "The Return of the Archons". The Starship Archon was sent to Beta III a century before. We don't know what the Archon's mission was and we don't know what the crew of the Archon did at Beta III, but we can assume its mission was exploratory. Whatever the case, the Archon was obviously destroyed. Kirk was sent to investigate. Upon discovering that Beta III was a starship trap much like Eminiar VII, Kirk obviously had the authority to take action. Landru was a threat, and Kirk "took care of business".
None of this should be a surprise. TOS was, after all, a Cold War series and it reflected its times well. Does that make its conventions and philosophies disingenuous? I don't think so. You have to consider the philosophy behind the Prime Directive. Was it just meant to isolate non-aligned planets without question? Why would we assume that? If that were the case, the Federation wouldn't need manned starships to explore inhabited planets.
We don't know all the purposes and reasons behind the Prime Directive. We can readily assume that General Order One is meant to regulate the actions of exploring starship crews, but we can also assume that such regulation also protects the Federation from over-extending its resources. Beyond that, we don't know.