Let's say we accept an argument similar to a voter irrationality argument, but applied to the meat industry. I won't rehearse the argument in detail, but it's something like:
1. Given the extent of the meat industry and the amount of meat consumed by the average person, no single person's decision to stop eating meat will in any way affect the number of (we'll stick with cows here) killed over any given period of time.
2. Given this, no single person can, on their own, have any effect whatsoever on the number of cows killed over a period of time.
3. Thus, to stop eating beef for the purposes of saving the lives of cows is an entirely ineffective means to that end.
4. Thus, if one's sole purpose in not eating beef is to save the lives of cows, not eating beef is irrational.
OK, now, let's say that you accept the validity of this argument. Here's another:
1. It is worse to end the life of a non-suffering being than it is to end the life of a suffering being, at least in the case that one has no power to alter the amount of suffering in the situation other than through the being's death.
2. Thus, if one has decided to take a life, it would be better to take the life of a suffering being than that of a non-suffering being.
3. Thus, eating beef from a factory farm is prima facie better than eating beef from somewhere less tortury.
Of course, the conclusion here has two caveats. First, we are assuming that in eating meat one is taking a life at all; if the first argument is sound, this is not the case. Second, the ought generated by this argument is merely prima facie. It could be overridden by other moral considerations.
At this point, one might think that it just doesn't matter where the beef we eat comes from. If the first argument is to be believed, then we can have no effect either way, and thus barring the introduction of other moral considerations in favor of vegetarianism, eating meat, regardless of its source, is permissible.
But notice something: the number of cows killed in non-factory farms over a given period of time is much lower than the number killed in factory farms. Thus, when one purchases meat from a non-factory farm, one has a greater chance of affecting the number of cows killed than one does by purchasing meat from a factory farm. Of course, the chances still might be zero, but if non-zero, they are larger.
So, we are now in position for the following:
1. Assume that the only moral reason not to eat beef is for purposes of avoiding killing cows.
2. If Argument 1 is sound, then one cannot reduce the total number of cows killed by not eating beef.
3. If Argument 1 is unsound (because premise 2 is false), it is most likely to be because one can affect the number of cows killed in non-factory farms more easily than in factory farms.
4. Thus, if Argument 2 is sound, then either:
5a. It is impossible to affect the number of cows killed by not eating beef, and thus there is no moral argument (recall premise 1) for a single person to refrain from eating beef; or
5b. One can only affect the number of cows killed by refraining from eating non-factory farmed beef, and thus if one wishes to lower the number of cows killed, one has a prima facie duty to eat only factory farmed beef; or
5c. One can affect the number of cows killed by refraining from eating beef in all cases, though one's influence will be greater in the case of non-factory farmed beef. However, while other interests (such as the prevention of factory farming specifically) may override, one still has a prima facie duty to eat meat from factory farms.
If I am correct about premises 2 and 3, I think it most likely that either 5a or 5b is the case. But of course, we have something of an epistemological problem; we may be unsure of which actually is the case. If, however, we can rule out 5c (which I suspect we can, though I fully admit I don't have the numbers to back me up), then in the case where we are unsure whether 5a or 5b obtains, we ought to prefer eating factory farmed beef, since we will either be choosing one of two equally permissible options or will avoid killing non-suffering cows.
Even if 5c is still an option, however, we still have some reason to prefer eating the factory farmed beef, though I suspect many will argue that even the epistemic possibility that we are negatively affecting the factory farming industry overrides these other considerations. In that case, Herman, you may continue to ease your guilt with Chipotle.