I'm always amazed when I get into these conversations that people are not just unaware of the possibility that the Prime Directive applies to post warp cultures, but that's it's more than likely actually how it works depending on the forwarded arguments representing the truth.
JANEWAY: The one that’s made of binding principles. We have our own set of rules, which includes the Prime Directive. How many times have we been in the position of refusing to interfere when some kind of disaster threatened an alien culture. It’s all very well to say we do it on the basis of an enlightened principle, but how does that feel to the aliens? I’m sure many of them think the Prime Directive is a lousy idea.
Kathy is not a fan.
TORRES: Some day could be too late. There are only a few hundred of them left.
JANEWAY: I feel for the robot's plight, but what you are proposing is exactly the kind of tampering the Prime Directive prohibits. We know almost nothing about these creatures or the race that built them. What would be the consequences of increasing their population, both to their own civilisation and others in this quadrant. Who are we to swoop in, play God and then continue on our way without the slightest consideration of the long term effects of our actions.
TORRES: Captain!
JANEWAY: B'Elanna, I share your scientific curiosity and I admire your compassion, but the answer is no.
Kathy met Post Warp robots in possession of superior technology enough to kick her ass and the prime Directive still applied to them because their technology is only a benchmark for their development not a finish line.
SISKO: I've agreed to release him.
O'BRIEN: But sir, Tosk is an intelligent, living being.
SISKO: It's their custom, Chief. Under the prime directive, we have no right to interfere.
KIRA: What if Tosk were to request asylum?
SISKO: If he asks for it.
Sisko allowed space bastards to hunt a sentient being because it was a symbiotic relationship enjoyed by both sides of the hunt even though the hunted was probably going to be turned into boots and pants after they finally tree him.
YEDIQ: All eight are murderers. Three are multiple offenders. We're just thirteen light years from our system. I'd appreciate it if you'd take us back there.
JANEWAY: Actually, we were headed in the opposite direction.
YEDIQ: I could arrange for one of our ships to rendezvous with Voyager. It'll take several days. My prisoners will have to be strictly monitored.
JANEWAY: Commander Tuvok will help you make arrangements. (Tuvok and Yediq leave)
CHAKOTAY: Some of the crew may not be comfortable helping to deliver eight men to their deaths.
JANEWAY: I can't say I like it either but, we have a Prime Directive to follow.
Capital punishment is murder. Janeway made her entire crew complicit as co-murderers by feeding these prisoners into a murder machine. She had to stomach doing distasteful things while "helping" out some Postwarp aliens in trouble even though she violently disagreed with their beliefs, unless it's a black guy tied to a chair
CRUSHER: She has been conditioned since the day she was born to believe it's perfectly acceptable to exist only to please men.
PICARD: She was born to do this.
CRUSHER: And bred by those people to seal a treaty with a seductive coup de grace.
PICARD: All right, fine, good, let's throw the Prime Directive to the winds. Let's detain her against her will. Let's destroy any chance of peace between these worlds. Let's interfere in their society, their customs.
Jean Grey and Professor Xavier. How cool is that? But again the Federation was playing delivery boy for a post warp culture where the Prime Directive still applied as a reason to not interfere with that culture's social development even as a political relationship continued between the Federation and these/some specific empires.
PARIS: He's directing us to a system two point three light years from here.
JANEWAY: Is that your home?
BOMB/EMH [on viewscreen]: It's my target. The course I've plotted bypasses enemy minefields. Don't deviate from it. Your ship won't be harmed. Once we've reached the system you'll transport me to my target.
JANEWAY: We won't help you wage war. This crew has a Prime Directive that forbids us to interfere in the affairs of other species.
BOMB/EMH [on viewscreen]: You've already interfered.
JANEWAY: We were trying to help you.
BOMB/EMH [on viewscreen]: Until you discovered my true nature, then you tried to deactivate me.
Advanced warp capable AI that took over Voyager and leveraged the captain into acting naughty. Post Warp Culture, Prime directive. I'm seeing a trend.
ANEWAY: I'm still counting on getting this ship home.
KASHYK: Are you sure you'll be welcome when you do? I came across something else in your database. The Prime Directive.
JANEWAY: The Federation's cardinal protocol.
KASHYK: It seems you violated it when you rescued these telepaths.
JANEWAY: Well, let's just say I usually go with my instincts and sort it out later at the Board of Inquiry. Those Admirals and I were on a first name basis, you know. You're risking a lot, too. Why?
This is a big one.
What's the difference between a political prisoner and a terrorist? And if these terrorists/political Prisoners are being held by a nation/culture of complete bastards or saints? What's the difference between Auschwitz and Guantanamo Bay (wasn't that place closed down?). Janeway can't pick and chose. What ever the local power says is wrote is wrote. She broke the law of a sovereign post warp culture by helping criminals be criminal just like how the rail road used to take slaves up north back when the South had it's own opposing thoughts about the matter. She's not allowed to break the laws of even Space Nazis because that puts the entire Federation on their shit-list. If there's one shit-list you want to stay off, it's the Space Nazi's shit-list.
Also it seemed that Janeway believes that the old school tie and greasy gladhanding puts her above the law, that no court in the federation is unbiased nor fair enough to do much but give her a medal no matter how heinous and criminal her behaviour.
SISKO: They don't even know the Cardassians are involved.
CHEKOTE [on monitor]: Then you're saying it's a genuine political revolution internal to Bajor.
SISKO: Supported by the Cardassians.
CHEKOTE [on monitor]: But internal to Bajor. The Cardassians might involve themselves in other people's civil wars, but we don't. The Prime Directive applies, Ben.
SISKO: Admiral.
If the Prime Directive applies to Bajor, then it bloody well applies to everyone.