If that were all there was to it, I would agree. The complicating factor is that as far as Janeway and the crew knew, Species 8472 both intended to exterminate all life in the Milky Way Galaxy -- "the weak will perish" -- and had a realistic potential to do so (see their military success against the Borg). That does suggest that it's better to back the force that has so far not gone that far yet.
Now, once Janeway learns that Species 8472 are people who can be negotiated with, the calculus changes completely.
Janeway didn't really know they could be negotiated with until "IN THE FLESH" in season 5.
The turning point in "SCORPION" was when Chakotay found out the Borg started the war by invading fluidic space. Once Voyager went there and used the altered nanoprobe weapons, it was basically just a way to keep them at bay.
And of course, the Borg (Seven) tried to get them assimilated as soon as the threat was over. Being the scorpions they are, as Chakotay rightly pointed out.