Context is everything.
There is a big distinction between event's like what Sisko, what janeway did and what the others did.
In depiction, Janeway, and Sisko, are not depicted as being righteous for their actions. Janeway and Sisko are both shown to be way off their norm and acting in extreme manners.
Same for Archer during "Damage." Dude is pushed so far passed his breaking point and he's doing things out of absolute desperation to save the entire human race. That's what the not-so-subtle title of that episode is actually referring to. Not how blasted up the NX-01 is, but how badly the people on board are hurt by the events.
As to Picard and the virus, I know a great many people who think he was straight up wrong. Frankly, the entire episode is based on a false assumption anyway. Hugh is an anomaly in The Borg, not the norm. It's not prejudice to look at a Borg cube and go "Borg = Evil." Because they are. They're a cold, calculating machine that will rip you from your bed and turn you into them. There's no talk. There's no mercy. There's no distinction between civilian and military beyond use to the collective. Virus them til there are no borg left. This isn't about saving some vast and ancient culture, this is space cancer.
Still, as much as it's easy to play quarterback in a life or death situation... Laying an ambush when you're dealing with an enemy that doesn't fight "fair" is... Always a mixed bag, but sometimes you have to do, what you have to do.