Keep in mind that evolution works primarily at a subspecies level, so any mutations which benefited that lineage at the expense of the species as a whole would tend to be favored.
Actually, evolution is almost entirely dominated by selection at the individual level, with a modicum of kin selection thrown in. The notion that selection acts at other levels is highly speculative (I wrote a novel based on the idea, but it's the purest kind of speculative fiction: http://www.amazon.com/Darwins-Theorem-TJ-Radcliffe-ebook/dp/...)
Sounds like you're agreeing with me? By "lineage" I'm talking primarily about the lineage of a gene, or in many cases the so-called inclusive fitness of an individual.