While there were clearly mitigating circumstances during the Voyager's time in the Delta Quadrant the many crimes of Captain Janeway surely would not stand up to a board of inquiry. In the maiden voyage of Voyager she violated the Prime Directive in denying the "Array" to the Kazon in the interests of protecting the Ocampa also stranding herself and her crew in the Delta Quadrant. Thus begins a sequence of events that see her handing over her vessel to the Kazon, wiping out thousands of ships containing sentient beings, handing technology over to the Borg Collective, giving the Hirogen Holodeck technology, and even an instance of killing a fused member of her crew known as Tuvix. This is not to mention the time traveling shenanigans VS the Borg by a future Admiral Janeway who presumably should have also been court martialed in that timeline.
Not enough evidence. Most of the crew were unwilling to testify out of fear of being prosecuted as accomplices (or fear of Janeway herself), and many of the records of Voyager's escapades were conveniently lost during the estimated 109 times the ship was nearly destroyed.
I can't believe you people. Captain Janeway was a goddamn hero that led her Crew and her ship through a completely uncharted Quadrant of Space! Of course she couldn't play by the rules if the rules were only tailored to (Federation-) charted space!
She was unorthodox in her methods, for sure, but didn't she bring most of her crew home safely? Didn't she establish relationships between the Federation and countless alien civilisations?
This isn't a call to disregard federation rules and laws on a whim - they're there for a reason. But If the parameters of a situation are changed, you have to adapt. Janeway knew that, as did many Captains before her!
Source:
Janeway, Kathryn (2380). "In unknown waters. The Journey of the Voyager through the Delta-Quadrant". University of Cambrige Press. Earth
Janeway also waged unprovoked war on an alien race, and attempted to use biological WMDs to commit genocide. She really was a war criminal.
When you are any position of authority your first and foremost objective is to keep your crew safe. Everything Janeway did in one way or round about another kept either herself, her crew, or the people that lived on Earth safe. I mean if the Federation really expected Star Trek captains to NOT defend themselves or the people they care about safe then why give them massive weapons on their starships? Why have photon torpedoes and ship phasers that can destroy most ships in the blink of an eye? Why have an officer dedicated to tactical and evasive maneuvering? Diplomacy can only get you so far. Sometimes the only thing some people understand is how much might you have at your disposal and how they can separate you from that might whatever it might be.(as in the case of the Hirogen)
Janeway found peaceful solutions where none seemed to be had. Take the episode Counterpoint for example. Janeway found a way to be humane to a section of a society who asked for their help(she didnt go out of her way to seek them out or coldly tell them that the Prime Directive forbade her interference) who were persecuted by another section of that society who would have wiped them out without remorse. Yes she had to use deception but she herself was the one trying to be deceived by the Devore inspector, Kashyk. She didnt have to find a peaceful solution but she nonetheless in the end did.
My last point is when the Caretaker pulled the Voyager crew into the Delta Quadrant it was against their will. I would say everything that Janeway had to endure was under the duress of the Caretaker's first actions. From the destroying of the Caretaker's station to keep it from the Kazon to blowing up the Borg hive none of it would've been possible had the Caretaker not put Voyager in that situation to have to make those decisions. It would be as if someone who lived now in modern times were teleported back to the days of the wild west. Would you try to continue to live as you do now or would you dress and act like the locals in order to fit in and not get yourself killed? She did as well as she could in the situation she was presented with in the environment that she was forced into. Janeway upheld the Prime Directive as much as she could in counterbalance of the trip of getting her and her crew safely back home. She was not in the Alpha Quadrant. The Alpha Quadrant rules did not take into account being forced to another quadrant and dealing with the denizens of that space. With that said Im not even sure the Prime Directive would apply in this case since they were pretty much out of the bounds of the enforcement of said Directive.(Starfleet could not send ships to the Delta quadrant to rescue them or enforce the Prime Directive) As I have said Janeway enforced Starfleet rules as her situation would allow. She should have not been accountable for violations that were not necessary.