Well many arguements can be made for both sides just as you have done though, but it doesn't make it any less true. Just because our evolution is at a different stage than animals doesn't mean we have souls and they don't. Just because they don't act the same way we do, or use our technology, doesn't mean they don't have souls. Ants for example are extremely efficient, well organized, etc. for what they do. For all we know, their interactions to them are just as devoloped as ours amongst ourselves. Who knows, maybe one day there will be something else out there that is way more capable than our homo-sapien race. These are just things we don't know, and can't predict.

The only reason it is alright for people to kill cows, etc. is because we, the people condoned it long ago, and just accepted it. There was once a time when people would kill other people and not think twice about it or the reprocussion, if there even was one. That doesn't mean that person didn't have a soul, it just means that laws and rules of conduct, ethics, etc. weren't set in stone yet. Times change, that is all I'm saying.