I'm actually watching Scorpion right now, and it's clear that they have full intent of destroying life that is weaker than them.
I haven't seen In The Flesh since it first aired, but based on my vague memory, the borg attacked them first. So it seems to me that Species 8472 were originally intending to wipe out all life in the quadrant out of revenge for the borg's attack on them.
So, my guess is, if 8472 had defeated the borg, they probably would have gone on to attack non-borg worlds too. But that's a good question and an answer is never really given.