This question assumes that the End All Suffering refers to humans only. However, we consider it as a much broader solution to a much broader problem, which humans are the absolute worst symptom of. We view suffering as the problem, and sentient life is its root cause (see Why Nonhumans Too in the FAQ, Non-Speciesist Suffering in the article section and The Violence Even Activists Are Disregarding in the Blog).
But even if “only” the human race is annihilated (if for example one of the research groups would find such an option feasible in the immediate range and decides to execute it), there isn’t much doubt that the fate of the captive animals will be much better anyway. In that scenario unfortunately they probably would die from dehydration or hunger, but as horrible as it is, it is still much better than their current lives. Even the last phase in their miserable lives - the aggressive and traumatic snatching from the shed, loading into the truck, transportation, violently forced into the slaughterhouse and the slaughter itself, probably cause more suffering than the suffering caused by death of dehydration or hunger. Not to mention whole lives of suffering in every single moment.
If the End All Suffering idea isn’t carried out, the caged animals would stay in the cages anyway and continue to suffer from density, suffocation, beating, humiliation, dehorning, number burning, dehydration, starvation, rape, ear clipping, force feeding, castration, boredom, diseases, transportation and slaughter. Nothing is worse than factory farming.
Do you really doubt that a death from hunger is less horrible than a year in a battery cage? Than six years in a cow shed? Than ten years in a circus? Than 20 years in the premarin industry? And in most of these exploitation industries the exploited animals are suffering from hunger and dehydration anyway.
Even if you insist that many animals will endure more suffering in the cages after the human race is gone than while humans used and abused them, this question regards the captive animals who are alive after the annihilation only. Every year the animal exploitation system breeds 150 billion more animals to suffer from birth to death. So after a few months only, the suffering that is prevented by the annihilation will be much greater than the suffering of the captive animals living after it.
The annihilation idea is for good. The above argument is relevant to one generation only and as we explained, even for that one generation it is better. What about the future generations?
Things are only getting worse. The global animal consumption is growing rapidly and persistently. Every year more animals are being exploited. And it is not only a quantitative matter, every year the industries make the exploitation more efficient on the expense of the animals’ broken bodies. The genetic invasion is getting more harmful and violent every year. Farm animals are already genetic freaks - born to be cripples.
The next generation will suffer more than the present and less than the one after it. In the future, many more animals will suffer much more.
We hope that the process causes as little suffering as possible.
But remember that no matter what the method is, it will cause suffering for one generation only (in the case of captive animals) and then the suffering (at least the human caused one) will be stopped. So even if your annihilation idea has a potential of causing a lot of suffering, there is no doubt that it is still worth it because nothing can be compared to the suffering that a decision not to do it will cause. Otherwise the suffering will never end. Generation after generation will be born to this cruel world as the new sufferers, only to become a steak, omelet, shoes, coat, sweater, pillow filling, decoration, an entertainment object, or the food of humans’ food.
If you are thinking that it is wrong to "sacrifice" a generation (and as we wrote, we don’t see it as sacrifice, especially for the animals who are living at the time of the annihilation, since the lives of most of them is suffering from birth to death) for the sake of all the sentient beings that will ever suffer on this planet, we ask you, don’t you think it is wrong to "sacrifice" all the sentient beings who will ever be born into a life of suffering from birth to death?
When you decide not to "sacrifice" one generation, of which billions are suffering every single moment as it is, you condemn uncountable number of sentient beings to a life of suffering from birth to death.