Observe that Coyne's criticism centers on words like "truth" and "answer".
"Science works, bitches" -- to answer particular types of questions which have certain properties. Questions about ethics (that is, what one "should" do) can be informed by science, but there is no such thing as a falsifiable ethical framework; an ethical framework must by its nature involve assumptions which are not determined by science.
Thus, an "answer" or "truth" within ethics is a different type of thing than an "answer" or "truth" within, say, chemistry. Coyne glosses over this by assuming the only type of "answer" or "truth" that matters is the type that comes from science or can be verified by science. This is not an isolated misstatement; he has previously said that "Only science has the ability to answer questions" [0]. Rather amusingly, this is a philosophical and non-scientific assumption.
This is why Coyne's response is essentially useless. Science is an awesome tool, but there are questions it can only address within a framework dependent on non-scientific assumptions.
[0] http://vimeo.com/31505142 around the 34:20 mark