WHilst she does have a responsibility to her crew, she has a larger responsibilty to the Federation as a whole. Given that consideration was it the right decision?
As I think about it more, Janeway never saw species 8472 (The Undine?) attack non-borg targets, with the exception of her ship and crew (Voyager was parked next to a cube though.) So based on what she saw, 8472 wasn't butchering innocent species. did 8472 ever say (telepathically or otherwise?) that they were going to destroy the Galaxy? and if memory serves, there was a later ep. where 8472 had some elaborate facility mimicking starfleet academy for training purposes, and Chakotay would up making peace with them or something. So, what it boils down to is Janeway makes a snap decision that affects billions or trillions of lives...but all she cares about is her 150 crew, and a ship that even if the borg had assimilated they wouldn't had gained anything useful, because if Janeway had half a brain, if Voyager was getting assimilated she would have some auto program that would wipe the main computer, fill the air on board with a fast acting painless toxin, and then distruct the ship 5 seconds after that, to prevent the nanite cure from falling into borg hands.