Here are the deleted scenes from the "Omega Glory" script. The following scene starts immediately after Tracy tells the landing party that they will never be able to leave the planet.
INT. MEN'S HOUSE - ANGLE ON CHARCOAL BRAZIER - DAY
CAMERA THEN PULLS (OR CUTS) BACK TO REVEAL a pair of ELDERS, richly dressed and obviously men of some importance, sit there eating strips of food being broiled at table-center on the charcoal brazier. Also ESTABLISH the room as Tracy leads Kirk in, followed by Spock. It is a large interior, serving the Village men as a place for food and drink, plus recreation over some game tables peculiar to Omega. The VILLAGE MEN inside respectfully clear a path to a large and more prominent table. Seeing Tracy approaching, the Elders get hurriedly to their feet, move on, leaving the brazier table to them. Some attractive SERVING GIRLS put out fresh dishes and cups. During which . . .
TRACY: Quarters are being prepared for you. And a place for Dr. McCoy's equipment to be beamed down to him.
Kirk has turned toward one of the Serving Girls and she jumps back in terror, dropping her dish. Tracy motions her back in.
TRACY: They were afraid of me at first too. It's our white skin . . . Our similarity to the Yangs, the white savages.
CLOSER AT TABLE
As Tracy sits, something of the feudal lord in the way he ignores the highly respectful nods and greetings given him by the villagers. We can see Kirk and Spock have exchanged looks, interested at this extreme deference and the Exeter Captain's casual acceptance of it. Tracy accepts food from one of the girls:
TRACY (to Kirk; ignoring Spock): Barbecued wild game. Sort of a long-necked rabbit-antelope.
Tracy motions and the Girl spears a strip of meat from the fire, extends it to Kirk. Meanwhile the other girl has hurried in to supply crude pitchers of liquid, plus fresh strips of meat on the brazier.
SPOCK: You are treated with considerable deference by these villagers, Captain. Almost a 'leader' or a . . .
Again, Tracy ignores Spock, interrupting:
TRACY (to Kirk): These Kohm villagers asked for help, Jim. Whatever spirit they may have once had has been whipped out of them by the savages.
KIRK: The Kohm villages are all under attack?
TRACY (nods): This is one of the last. But before the Yangs began decimating them, they apparently had a considerably advanced civilization. There are ruins of large cities out there.
SPOCK (now to Kirk): Nomad tribes are sometimes able to destroy advanced civilizations, but not unarmed savages. (to Tracy) Are you quite certain, Captain, that . . .
EMPHASIZING TRACY
To his feet, angrily facing Spock and interrupting.
TRACY: I will not be questioned by a subordinate.
Spock remains completely unperturbed, eyeing Tracy curiously. Kirk speaks quietly, a little more formally now:
KIRK: Captain . . . I think you're forgetting that Mr. Spock is my First Officer.
Mr. Spock gets to his feet. Quietly and politely:
SPOCK: I see no purpose in causing anger to Captain Tracy. May I remove myself?
Kirk hesitates, then nods. Spock moves quickly outside. Kirk turns back to Tracy coldly.
KIRK: Let's clear something up right now. I never had a better 'First' than Spock . . . or a better friend.
TRACY: I've yet to meet a Vulcan capable of understanding friendship. He's certainly doing his best to sabotage ours.
CLOSER TWO SHOT
Tracy showing some bitterness.
TRACY: You know what's on his mind, too. Your 'friend's' computer mind adds up a few scanty observations and he's suddenly convinced I've violated the Prime Directive . . . that I'm interfering with this culture.
KIRK: Ron, a first officer's job is to be suspicious. (smiles) Saves his Captain from having to appear the villain.
TRACY: I'm a fellow star captain. Ask.
KIRK (beat; nods): Fair enough. The local militia recognized what our phasers are. Also, they seem to accept orders from you . . . (hesitates; then) I am not making an accusation. As you said . . . I'm asking.
EMPHASIZING TRACY
Studying Kirk, then:
TRACY: All right. As long as we're asking . . . suppose you were faced with incredibly vicious savages massing for a final attack that would wipe out the last trace of civilization on a whole planet. (indicates) And suppose you had enough phasers to stop it? Can you imagine the power of just five phasers in this culture?
KIRK (nods): Like introducing the atom bomb into the gunpowder era.
TRACY (leans in; intent) Jim . . . within 48 hours they'll slaughter every adult and child in this village . . .
KIRK: Every time man interferes with the natural evolution of another world, he destroys more than he saves.
TRACY (snaps): When they attack, Jim, we've no place left to go. We're finished too!
KIRK (beat, quietly): 'I solemnly pledge I will abide by these regulations, even in death.' (beat, shrugs) Unfortunately, that's the oath we both took.
TRACY (nods): And, you'd try to stop me.
KIRK: I wouldn't 'try', Ron. I'd stop you.
The foregoing was replaced in the aired episode by a brief log by Captain Kirk, in which he merely aired misgivings about Tracy having violated the Prime Directive.