Discounting other theories unjustifiably, or overusing a particular theory past it's explanation is one sin. Not understanding a theory is another however. I think that many people who draw such false conclusions still base them on a pretty clear understanding of the core of evolutionary theory, i.e. mutation, gene exchange, selection, reproduction.
I understand that I am incorrect, my own self-doubt was not made sufficiently clear. I do not however agree with the fatalism that I perceive in the initial quote. To me it seems to suggest that understanding evolution is impossible. I guess this is not necessarily the appropriate place to look for information on evolutionary theory, but nonetheless I do not agree with the suggestion of unassailability of understanding, if that is what's going on.
This may be fatally sophomoric, but I really don't understand what is so particularly hard to understand about the theory of evolution. Differentiation, Inheritance, Mutation, and Fitness produce a feedback loop of increasing Fitness. The particulars of it's implementation on Earth are far more complicated, but the underlying theory is beautiful in it's elegance and simplicity.
I think that often people believe other things that crowd out the true explanation, so in practice it isn't applied correctly to real-world phenomena. Then, perhaps they try to reintegrate everything under a unifying theory of "evolution".
Anthropomorphism, promiscuous teleology, not understanding the level of selection, absolutist ideas about fitness, belief in a certain philosophical type of progress, etc. are culprits.
After all the misconceptions are added, the only work left for evolution is to provide a label for the jumble!
The problem with flipping the coin is that it already asks you to make an uncomfortable judgement about the values of John and Lisa's lives. You have already said "Our lives' values are comparable enough to merit coin-flipping". Acting out of the view of the partner gives the sort of mutual plausibly deniability that allows you to both percieve that the partner values your more than themselves.
I imagine you intended to link to consilience the concept, not the book. Then again you may just be trying to be subtle.