The Omega Directive doesn't exist... To %99.9999999999 of the people in the Federation, and there's a lot more recurring 9s if we want to only talk about how people in Starfleet don't know about the Omega Directive.
The Prime Directive is their highest rule that they're not ashamed of.
General order 12 is to melt the surface of a planet if the Captain doesn't report back to he ship in 24 hours.
General order 12 is fricking Genocide.
How many general order 12s can a ship follow though with, before there's a board on en enquirey?
These are not squeamish people.
Janeway said in Counterpoint that in the case of a Prime Directive board hearing that she can outwit any jury of Admirals becuase everyone in the Admiralty is her best friend and they love her enough to let her get away with murder.
Kathryn is really out of touch with who she is, this captain is not a protected and adored flower who can do no wrong no matter how bloody her cute hands are, this middle aged monster is a furious rancour who scares the willies out of the sternest souls, and if she tries that tact with her bosses, whatever good karma she built up earlier by being the daugter of a good soldier is going to be spent quickly.
The Delta Quadrant changed her.
She has become a savage.