I'm of the opinion that Ransom could have accused Janeway of being a criminal as easy as she did. 3 of the 4 episodes before relativity were more than enough to strip Janeway of her command and uniform.
Warhead. Prime Directive Violation. They perverted tech (an AI) into creating a conscience and stopped a single strike in a war that changed the outcome, losses and or duration of that war which Janeway had no right to involve herself in.
Relativity. Temporal Displacement Policy (DS9 past tense.) (The temporal Prime Directive doesn't exist in the 24th century "sometimes".). Aiding and Abetting. Considering the future is some times full of evil assholes and it's hard to tell friend from foe and it's so easy to be used like a donkey by an evil mastermind even if they're expecting you to rebel and do the exact opposite of everything they say (Note Archer's relationship with Future Guy and Daniels.) which is why they tell you to do every the opposite of what the need you to do (Shades of princess bride no?) ...You're sopposed to ignore future people, not jump through their hoops like trained seals.
Juggernaut. Prime Directive Violation. The ecological disaster resulting from the destruction of that juggernaught would either force the Malon to act responsible of force a nieghbour to kick the shit out of them until they act responsible or they die, whether that be from war or choking on their garbage, but you don't reward idiots endangering the universe with second chances and higher orders of technology if inside they're still assholes without any civic sense of responsiblity to take care of their own environment. This goes double for in Night when janeway tried to force recycling tech on the malon but they couldn't see the profit in not poluting.
Ransom handled the situation badly, but Janeway was just as big a criminal.
In Warhead, they interfered by freeing the warhead in the first place, so by stopping it they were only fixing their own initial error. The blame here is on Harry for beaming it aboard. I thought that was very clear in the episode. I don't see this as a big violation on Janeway's part. This has happened in every Trek series. They make a mistake, then they have to correct it.
Juggernaut is a legit breaking of the Directive. The difference here is that they helped clean up to stop the tanker from polluting an entire system. It does break the Prime Directive, but it was in the interest of saving many species from the interference of another. Voyager had no place to interfere though.
As for Relativity, I prefer not to debate time travel episodes. Too many inconsistencies. There may or may not be an issue, but I'm personally willing to just give Janeway the benefit of the doubt here, as Voyager doesn't seem to acknowledge any temporal prime directive in the 24th century.
She has definitely broken the Prime Directive on many many occasions, no doubt about it. The difference is that she mostly did it for the benefit of other races, sometimes even at the expense of her own crew (even if she was misguided at times). The crew of Equinox were violating the Prime Directive for nothing other than selfish personal gain, even though it was blatantly at the expense of another race.
I'm not sure how bad they compare to each other in Starfleet's eyes, but morally speaking, there is no comparison between the two imo. We're talking breaking the PD by killing aliens vs breaking the PD by saving them.
