I'm not a vegan, but I've heard this argument before and find it to be confounding. Are we saying that livestock suffer less because they are safe in the knowledge that their species is being conserved? Why would a non-human animal have this kind of existential rumination? (Excuse the pun) And let's say this concern is of real importance, if factory farming ended do you think wild populations of cows, goats, etc. would go completely extinct? (Keep in mind people keep animals as pets, so that's also another means of conservation)
As for wild populations, I'm not sure, but my understanding is that most cows have been bred to produce more milk than their calves eat, and that their udders become painful if not milked; and that sheep's hair tends to similarly grow much more than in wild breeds, leading to major problems if they are not sheared by humans. I may be wrong, and even if I'm not they may still live long enough to breed and perhaps reverse these artificial adaptations in a few generations.