While some animals do exibit adoption, I don't think its nearly as common as altruism towards biological children. And group membership that requires altruism overwhelmingly seems to have genetic tie-in.
For this to happen across, say, two genetic lines, it seems you need the "cross-altruistic" genes to emerge more or less simultaneously in the two groups so they can cooperate. The probability for this to happen is smaller, so it's not surprising that it happens less often than kin-style altruism. But if this does happen (and apparently it does), then it means kin selection is not enough to explain altruism.
It seems to me that Wilson's theory is an elegant generalization of kin selection. I don't see the contradiction between them, although I'm not a biologist so quite likely I'm misunderstanding something.
This premise seems to be taken as fundamental dogma in the evolutionary theory community, but perhaps should be questioned. Here is my (layperson's) counterexample: a species might have a gene that switches between whether an individual is a drone or a reproducer over the course of their life; a switch like that could thrown early in the development based on ambient hormones or whatever. If the individual is not a reproducer, they don't spread their own genes but they help the hive or whatever.
I think there is an unexamined assumption guiding contemporary evolution, that ALL behavior must be explained by genes ALONE -- in the case above, lifetime behavior is determined by an environmental trigger, even though the set of possible behaviors is determined by genes. This dogma seems, well, silly and wrong.
(Throw in cultural behaviors with outcomes like longer life and more offspring, and the classical system completely falls apart.)
Genes that encode specific behaviors are just the simplest possible mechanism that works, and they do account for a vast number of phenomena. I think Occam's razor applies: If you suggest a more complicated mechanism, you should have some supporting evidence.
On the other hand, members of a herd are usually genetically related, so it is possible that kin selection can also explain this phenomenon.
Wilson isn't proposing they are mutually exclusive, he is saying they are both right but to differing degrees.
It's common in the sense that symbiotic relationships are common across ecosystems and probably a definitive element of what makes them a "system".
Stephen Gould took the idea further in his idea of "hierarchal evolution". Evolution isn't just happening on the genetic, individual, group, and species levels. It's happening at every level of organization.