You can't fix rape with more rape.
If the non interference directive and, if it isn't the same thing, the Prime Directive applies to the Klingons, an ally and trading partner who the Federation spent 200 years at cold war with, exactly how does Janeway think that the Ocampa are exempt?
Their natural development is always developing, their recovery, restoration and reconstruction after Caretaker fucked off could have unfolded in many different ways, that in a dozen generations that these peoples descendants would have been assholes or saints, depending on the nature of their environment and resources. Were the kazon going to have godlike Caretaker powers, or were they going to be Feudal scum BBQing Ocampa sausages on Sundays getting pissed with their pals? Were the Ocampa going to be a slave race to the kazon for food, or were the Kazon going to ignore the muchkin shortlifers until they all starved to death... Or did Janeway leave them weapons or show them how to turn the Caretaker technology threaded through their city into powerful weapons that the Ocampa became a spcies of despotic warlords conquering known space under an iron heel?
The Prime Dirctive absolves the Federation from the resposibility of creating assholes and victims.
Yes Overlord, the flip flopping. Sorry, you were right of course.
However in the case of Time and Again all Janeway did was stop Tuvok's rescue attempt which was was going to blow up the planet. It's been a while, but you're right that she would have already have had to have gone ballsdeep against the grain of the Prime Directive to figure that out, but considering her own Security Officer destroyed that world, and not the aliens themselves... If it wasn't for the timetravel component she would have been in the right to save them from her own command (That's Dukat! "I am a good man who deserves "thanks" an statues because I didn't kill all the Bajorans when I had the chance!"), external influence socially, but internal influence temporally, (time trumps space?) because these aliens could go on to innocently sell this armaggeddony technology to a thousand worlds who all blow up in the next decade, so it was a boon to the neighbourhood that they got turned to ash (Similar to how the Federation gave that toxic tech to aliens in Friendship One.).
This was exactly the same as Caretaker (She sad that the kazon could have the Array after they had finished with it and that she had no claim on the technology and that she was neutral but the kazon didn't believe her, so they fired on Voayger) Kathryn tried to follow the Prime Directive until she felt guilty and complicit. Janeway didn't start out in each of these episodes thinking that the Prime Directive was stupid, she just gradually came to the conclusion.