I respond in the "source", because the characters limit is very annoying.
"The only way a species can be altruistic by nature is through its evolution."
Yes, i strongly agree with it.
"My argument more-or-less describes the mechanism by which such traits are selected for."
You are assuming evolution select for behaviors that improve the individual circumstances, but this is false, evolution select for whatever genes spread the best, it can largely overlaps with behaviors that improve the individual circumstances, but it is certainly not the same thing.
Evolution can select for genes that make the individual worse, it can even select for genes that bring the entire species to extinction.
See it : http://lesswrong.com/lw/l5/evolving_to_extinction/
"Whether it's conscious or not, it's likely that's the reasoning behind altruism."
Here is where i completely disagree, evolution select for behaviors that spread genes effectively, not for a complex understanding (conscious or unconscious) of how some behaviors will spread genes effectively. Firstly because this understanding is way too hard to acquire through natural selection, you need science to understand it, and secondly because it would be useless to know why a behavior spread genes, the individual only need to have the behavior, understanding why, consciously or unconsciously, would mainly be a waste of resources and be selected against.(if not like a epiphenomenon of rationality)
Yes, natural selection, had selected for empathy, for reasons completely blind to empathy, but it still had selected for a genuine empathy.
Nowhere in the brain of most individuals, there is a thing that calculate how empathy will be self-beneficial, firstly because it is useless in a evolutionist point of view, secondly because evolution don’t primarily select for what is self-beneficial (otherwise most animals would not die so young).