Two things: first, kin selection is one possible mechanism by which a critical mass of cooperators can arise, but it is not the only such mechanism. And second, the mechanism that gives rise to cooperation may have evolved for some other reason, with cooperation as an ancillary effect.

For example, inter-species cooperation (as between dogs and humans) is almost certainly not a result of kin selection.

So even if Wilson is right and the theory of kin selection is flawed (I can't imagine how he could be right, but I haven't read the paper) that is not an indictment of Axelrod.