Kes made telepathic contact with Species 8472 and knows that they plan to purge all life from our galaxy which they view as 'unclean'. She tells the Voyager crew this. Who started the war is fairly insignificant compared to this. The fact remains that Species 8472 have no intention at stopping with just defeating the Borg.
Has Starfleet's position on helping one species annihilate another generally rested on one crew member having a bad feeling about them??
Therefore, by your reckoning, if Janeway hadn't allied with the Borg then Voyager would potentially have been responsible for the end of all life in the galaxy.
As it stands, again by your reckoning, they are actually responsible for saving all life in the entire galaxy with the exception of anyone assimilated by the Borg.
You're ignoring "in the flesh" (wish i could) but sorry, it happened. Species 8472 are not malevolent destroyers intent on purging our galaxy. They're actually very reasonable, articulate and considerate and sweet and funny etc etc
The fact that they're really pissed off with everyone in non fluidic space just after they've been attacked by a species (the Borg) from non fluidic space, is hardly a convincing argument for saying that they're pure evil
Imagine if you came home to find your mother violently beaten by a man who's running away down the street and you shout...."i'm gonna f**ing rip your face off". Does that mean the neighbours who hear you shout that should assume that you're a violent face ripper at all times without any exceptions
"In the flesh" made Kes look like an idiot and made Janeway look psychotic for basing such a violent, damaging, genocidal plan on the confused mental abilities of a child
Oh and it made species 8472 suck too
But like it not......it happened