I'm wondering how effective would the pathogen had been if Voyager had opted to use that rather than the events that ended up playing out in the episode? We learned in episode "Child's Play" that Icheb was genetically engineered to produce this pathogen. I would think he would be immune. He was also in a small Borg collective with the other Borg children. That leads me to believe that the children were already being exposed to this pathogen from Icheb and if that pathogen could affect them it would have already.JANEWAY: A pathogen.
EMH: A space-borne virus that adapted to Borg physiology. It's inert now, but in its virulent state it attacked the drones and killed them.
TUVOK: Why weren't the juveniles infected?
SEVEN: The maturation chamber is designed to protect developing drones. Malfunctions caused by the deaths of the adults led several of the chambers to open prematurely.
TUVOK: Does this pathogen only target the Borg?
EMH: The Borg, and other cybernetic organisms it encounters. You're not thinking of using it as a biological weapon?
TUVOK: If we can revive the pathogen and reintroduce it, we could neutralise the drones without harming the away team.
EMH: Neutralise? You mean murder, don't you? Captain, they're children.
Leaving the question about whether the plan to use the pathogen in order to save the hostages would have worked or not?