The difference is that Sisko's behaviour was consistent and built on personal treachery.
So was Janeway's. She made no secret of her dedication and loyalty to Federation principles and human morality numerous times.
And yes, it was personal treachery. Janeway clearly states she knew Ransom before this whole mess, and she got to know him better before he betrayed her.
Conversely Janeway went of on some half cocked crusade because she was personally offended at Ransom's lack of commitment to Starfleet values. Sisko had his trust betrayed and his command undermined by Edditington. In fact, if you watch "For the Uniform" closely, you realise that its not about the Maquis....he'd dealt with them before....it was about Edditington.
"Half cocked?" She had evey right to be angry. Ransom had committed genocide, betrayed the uniform, undermined Federation values, and betrayed Janeway;s trust and her crew to save his own neck. And if you watch Equinox clearly, you'll see Janeway let her restraint in bringing Ransom to justice go away, showing it was also about her personal sense of anger and betrayal along with her dedication to Starfleet.
The whole thing boiled down to Janeway being offended that someone broke Starfleet regulations.
She was more than offended; she was outraged, and you could see it was being held in. And again, Ransom did more than break the law; he threw morality and ethics to the wayside and murdered innocent sentients for his own gain. Gee, I guess some were a bit offended when Stalin began his brutal persecution. No reason to be outraged; all he did was break a law or two or three.
Indeed, one of the more disturbing elements of the episode was that Janeway never ONCE considered the situation that the Equinox crew found themselves in.
I'm pretty sure she did, and still came to the same conclusion; nothing justifies mass murder. The ends don't justify the means, especially in that case. Indeed, Janeway found herself in similar situations too, where she could have broke principle or her values to benefit her and her crew, but she didn't.
[She never once took the time to temper her anger by considering the extrordinary circumstances that these lost, battered people experienced.
Yet, these people finally did have a refuge, and chance to end their muderous ways (finding Voyager). Yet they don't care, and in the process leave Voyager to die. I'd be angry too.
[She never listens to Ransom's plea about watching his crew starve and die. Janeway just came of as an obnoxious prick with more compassion for unknown...clearly hostile...aliens than her own people.
She listened, and under careful consideration made the reasonable decision to let *gasp* his crew join Voyager, rather than say bye and good luck. Yes, curse that mean Janeway; she never offered them shelter, never considered protocol to see who had the final say, and to top it off she cut off thier access to showers and food...
) That's when the flirtation between the two of them stopped. (Trust me, watch the show again and you'll see it.)
