In order to understand this issue, we have to understand morality according to Buddhism. In Theravada Buddhism, morality is completely based on the effect that an act has on the mind of the actor. Hence, eating meat need not be karmically negative, yet killing Hitler to "save" others from suffering need be, since it requires defilement to take the life of another.
It is not considered immoral to do something just because it has negative consequences for others, nor does a positive effect for others constitute a sufficient condition for morality.
The reason for all this is that Buddhist morality is defined by its potential to lead to focus/concentration and eventually wisdom. One eats meat, knowing that the act is harmless, and so one's mind remains calm and the nourishment supports meditation practice.
The reasons behind killing our less evolved brothers and sisters - insects, spiders, foxes, etc., are inconsequential. Even if killing a single mosquito would end all cases of malaria in the world for ever, the (Theravada) Buddhist philosophy would be to abstain from killing the mosquito. Acting to prevent suffering can actually considered to be an unwholesome act, since it generally requires aversion to said suffering. In (Theravada) Buddhism, we act to prevent unwholesomeness, not suffering, since suffering does not lead to suffering, but unwholesomeness always leads to suffering.