The suffering of conscious creatures should be a guiding principle in assessing the morality of a system, and as such we should regard the factory farming of animals to be an abhorrent industry.
I would argue however that the actual humane *killing* of animals poses no such concern. This is based on the current psychological understanding that no animal has a capacity to imagine possible futures. True, a dog will get anxious if she recognises occurrences which usually take place prior to an unpleasant trip to the vets, but this does not imply an ability to actually plan ahead or to recognise future potential. The loss of human life is sad for a multitude of reasons, but much of the loss is found in the squandered potential. What could that person have achieved? More importantly to this theory, what did that person *hope* to achieve? What did they have planned or imagine ahead of them?
For as long as this isn’t a consideration in the death of animals I don’t see from where we can stand and state that it was a net negative to kill a cow when there are many millions more. Not only did it have no idea what might happen in the next minute, it didn’t much matter because the cow was never going to cure cancer or enact some other great good. In fact, the likeliest scenario is that the cow was going to fart and release methane into the atmosphere, and we have enough of that already.