Hypotheticals kinda lose their purpose if you're to account for everything that "might" happen. We simply have no basis to think the Borg could possibly find a way to defeat species 8472 on their own. They were at their mercy and Voyager saved them. His analogy is accurate.
I think he's confusing the future Borg episode or the episodes where the doctor gets his mobile emitter. Janeway is indeed not returning from the 29th century..she'd be long dead.