will you kill it?

Whoa. I didn't say that if I was living in factory farm, I would prefer to be killed. I might, and I might seek suicide, but that's a hard choice, because the will-to-live-above-all-else exists and is quite strong (for good evolutionary reasons). Also, approaching death is scary = suffering. So no, I wouldn't make that choice for another person, if I couldn't communicate with them and ask. If I could ask them, I'm not sure.

(This is a situation I've imagined myself in, i.e. if I have a patient someday who is able to convince me that they have made a rational decision that they want to commit assisted suicide. I can't model myself well enough to know what I'd do in that situation either.)

An individual that doesn't exist in the first place, i.e. because of better birth control or because fewer animals are farmed for food, doesn't exist to have to make a choice; at least that's how I see it. I could conceive of people thinking they're philosophically the same situation, but I strongly think that they aren't.

Are you willing to make that choice for others?

As opposed to what? I can't not make a choice. I can either buy meat, and choose for them to live a painful existence, or not buy meat, and choose for them not to. It's not as if I can offer them the opportunity to go back in time and kill their own grandfathers and make the choice for themselves.

Right, I meant individual (potential) animals existing in the future.

I don't think suicide is a good indicator here because we could imagine an evil scientist designing a mind that will constantly experience the worst feeling ever but that still wants to continue to go on living. Is it wrong to not prevent such a mind from being turned on? I strongly think so. Also note that evolution might function a bit like the evil scientist in the hypothetical, because evolution is all about optimizing gene-copying success and not about the well-being of individuals.

I think most people would agree that some forms of existence are worse than not being born, especially if they imagine the torture as vividly as they can. (I think someone linked to footage from factory farms somewhere in this comment section.) An interesting question is whether there is a duty to procreate, assuming that beings will live lives that overall go well. I don't think factory farms qualify for that, even if we set the bar pretty low, but if they did, the evaluation would come down to population ethics, where things get messy because it has been proved formally that no possible solution fulfills some seemingly very conservative adequacy conditions.

But the reason we find such reasoning (about the babies) repugnant is that we don't actually believe that heaven and hell are real. Even the majority people who profess to hold these beliefs actually don't. So what we see is just babies being killed.

But what if heaven and hell were real things? What if it were the case that some or most people go to hell and suffer eternally, and we knew this, for a completely reliable fact, and also knew that murdered babies go to heaven? Don't you think our view of things might be different?

If Christianity were true, wouldn't this be the most ethical thing to do? It's only wrong because Christianity is not true.

It's much more like choosing not to have kids when you're in a situation where those kids' lives will be horrible.

I've never heard of anyone doing this, although it's within the realm of possibility, but this was the topic of one of my earliest comments on Less Wrong.